Near-IR glucose sensors

ABSTRACT

The present disclosure provides polymerizable luminescent dyes useful for incorporation into polymers. The dyes and the polymers can be used in sensing and imaging applications, for example, to provide accurate and optionally long term measurements of glucose in vivo. The present disclosure also provides sensors including the polymers described herein. The sensors can be implanted into a tissue of a subject and used for long-term or short-term continuous and semi-continuous collection of data of various biochemical analytes, optionally without the use of implantable hardware of any type and/or enzymatic and electrochemical detection methods.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims the benefit of U.S. Provisional Application Nos.62/439,363 filed Dec. 27, 2016 and 62/439,364 filed Dec. 27, 2016, thecontents of each of which are incorporated herein, in their entirety, byreference.

STATEMENT CONCERNING GOVERNMENT SUPPORT

This invention was made with government support under grant nos.NIHR01EB016414 and NIHR44DK101000, both awarded by the NationalInstitutes of Health. The government has certain rights in theinvention.

FIELD OF THE INVENTION

The disclosure is in the field of luminescent dyes, polymers andbiosensors.

TECHNICAL BACKGROUND

Diagnosis, treatment, and management of diabetes and certain metabolicdisorders require monitoring of glucose concentration in the blood.Despite many advances in the minimally invasive blood glucosemonitoring, the currently used methods are expensive, cumbersome, timeconsuming, and do not provide accurate, real-time blood glucoseconcentration information. Thus, a need exists for a better long-term,minimally invasive glucose-monitoring system. Doing so non-invasivelywith minimal user maintenance is essential, and sensor longevity of daysto months is crucial in actual user environments.

Such real-time, continuous measurement of glucose concentration in theblood can be achieved by the use of sensors inserted or implanted intothe tissue and measuring the signal generated by the sensor by a devicelocated outside the body. Luminescence provides a useful tool for thedesign of such sensors. The sensors, which are monitored opticallythrough the skin, require a highly stable dye with excitation andemission spectra in the near-infrared (NIR) optical window of the skin.These dye properties are crucial for the successful design of aluminescent sensor that can be implanted deep into tissue. Monitoringnon-invasively through the skin requires the use of dyes with excitationand emission wavelengths in the optical window of the skin(approximately 550 to 1100 nm) to minimize light scattering andabsorbance, and to achieve a high signal-to-noise ratio. Presently useddyes require excitation with light which is largely absorbed by the skinand the underlying tissue. Additionally, the currently available sensorsare made of rigid materials that vastly differ from the mechanicalproperties of tissue in which they are implanted, are bulky andinconvenient, and induce a series of biological events upon implantationthat ultimately culminate in the formation of a fibrous capsule thatwalls it off from the body.

A need exists for glucose-sensing compositions that are NearIR-detectable, particularly in vivo, and are suitable for long-term,minimally invasive implantation into tissues.

SUMMARY OF THE INVENTION

Disclosed herein are luminescent dyes, polymers including said dyes, andsensors including the polymers.

One aspect relates to a compound Formula I:

-   -   or an isomer, a tautomer, or a salt thereof,    -   wherein the dotted lines denote a bond or absence of a bond;    -   when the dotted line connecting R¹ and O is a bond, R¹ is CX¹X²        and R¹⁵ is absent; and when the dotted line connecting R¹ and O        is absence of a bond, R¹⁵, at each occurrence, is independently        H or C₁-C₆ alkyl, and R¹, at each occurrence, is H, optionally        substituted C₁-C₆ alkyl, optionally substituted C₂-C₆ alkenyl,        optionally substituted C₂-C₆ alkynyl, optionally substituted        C₂-C₁₀ heteroalkyl, polymerizable moiety, NIR dye moiety,        electron-withdrawing group, or electron-donating group;    -   X¹ and X² are independently H or C₁-C₆ alkyl;    -   R² is H or C₁-C₆ alkyl;    -   Z is a C₆-C₁₄ arylene optionally substituted with R¹¹, R¹², R¹⁴,        and L²R¹³;    -   R³, R⁴, R⁵, R⁶, R⁷, R⁸, R¹¹, R¹², R¹³, and R¹⁴ are independently        H, optionally substituted C₁-C₆ alkyl, optionally substituted        C₂-C₆ alkenyl, optionally substituted C₂-C₆ alkynyl, optionally        substituted C₂-C₁₀ heteroalkyl, polymerizable moiety, NIR dye        moiety, electron-withdrawing group, or electron-donating group;    -   R⁹ and R¹⁰ are independently H, C₁-C₆ alkyl, polymerizable        moiety, or NIR dye moiety;    -   L¹, L², and L³ are independently a bond or a linker group; and        the compound includes one or more NIR dye moieties and one or        more polymerizable moieties.    -   In some embodiments, the compounds have the structure of Formula        IA, IB, or IC:

or an isomer, a tautomer, or a salt thereof.

In some embodiments of the compounds disclosed herein, theelectron-withdrawing group is selected from the group consisting ofhalogen, C(O)R′, COOR′, C(O)NH₂, NHC(O)R′, C(O)NR′R″, CF₃, CN, SO₃H,SO₂CF₃, SO₂R′, SO₂NR′R″, ammonium, alkyl ammonium, and NO₂, wherein R′and R″ are independently H or C₁-C₆ alkyl.

In certain embodiments, electron-donating group is selected from thegroup consisting of NR^(N1)R^(N2), OR′, NHC(O)R′, OC(O)R′, phenyl, andvinyl, wherein R^(N1), R^(N2), and R′ are independently H or C₁-C₆alkyl.

In some embodiments, L¹ is a bond or a linker group selected fromoptionally substituted amino, optionally substituted amido, —O—,optionally substituted —CH₂C₆H₄O—, C₂-C₂₀ PEG linker, optionallysubstituted C₆-C₁₀ arylene, optionally substituted C₅-C₁₀ heteroarylene,optionally substituted —C₁-C₆ alkylene-Ar—, optionally substituted—C₂-C₆ alkenylene-Ar—, optionally substituted —C₂-C₆ alkynylene-Ar—,optionally substituted —C(O)NH—C₁-C₆ alkylene-Ar—, optionallysubstituted —C₁-C₆ alkylene-C(O)NH—C₁-C₆ alkylene-Ar—, —(CH₂CH₂O)_(n)—,optionally substituted C₁-C₁₀ alkyl, optionally substituted C₂-C₁₀alkenyl, optionally substituted C₂-C₁₀ alkynyl, optionally substitutedC₂-C₂₀ heteroalkyl, wherein n is an integer between 1 and 10 and Ar isC₆-C₁₀ arylene or C₅-C₁₀ heteroarylene.

In certain embodiments, L² is a bond or a linker group selected fromoptionally substituted amino, optionally substituted amido, —O—,optionally substituted —CH₂C₆H₄O—, C₂-C₂₀ PEG linker, optionallysubstituted C₆-C₁₀ arylene, optionally substituted C₅-C₁₀ heteroarylene,optionally substituted —C₁-C₆ alkylene-Ar—, optionally substituted C₂-C₆alkenylene-Ar—, optionally substituted C₂-C₆ alkynylene-Ar—, optionallysubstituted —C(O)NH—C₁-C₆ alkylene-Ar—, optionally substituted —C₁-C₆alkylene-C(O)NH—C₁-C₆ alkylene-Ar—, —(CH₂CH₂O)_(n)—, optionallysubstituted C₁-C₁₀ alkyl, optionally substituted C₂-C₁₀ alkenyl,optionally substituted C₂-C₁₀ alkynyl, optionally substituted C₂-C₂₀heteroalkyl, wherein n is an integer between 1 and 10 and Ar is C₆-C₁₀arylene or C₅-C₁₀ heteroarylene.

In some embodiments, L³ is a bond or a linker group selected fromoptionally substituted amino, optionally substituted amido, —O—,optionally substituted —CH₂C₆H₄O—, C₂-C₂₀ PEG linker, optionallysubstituted C₆-C₁₀ arylene, optionally substituted C₅-C₁₀ heteroarylene,optionally substituted —C₁-C₆ alkylene-Ar—, optionally substituted C₂-C₆alkenylene-Ar—, optionally substituted C₂-C₆ alkynylene-Ar—, optionallysubstituted —C(O)NH—C₁-C₆ alkylene-Ar—, optionally substituted —C₁-C₆alkylene-C(O)NH—C₁-C₆ alkylene-Ar—, —(CH₂CH₂O)_(n)—, optionallysubstituted C₁-C₁₀ alkyl, optionally substituted C₂-C₁₀ alkenyl,optionally substituted C₂-C₁₀ alkynyl, optionally substituted C₂-C₂₀heteroalkyl, wherein n is an integer between 1 and 10 and Ar is C₆-C₁₀arylene or C₅-C₁₀ heteroarylene.

In certain embodiments, L¹ includes one or more substituents selectedfrom carboxylic group, sulfonic acid group, ammonium, and amino group.

In some embodiments, L² includes one or more substituents selected fromcarboxylic group, sulfonic acid group, ammonium, and amino group.

In some embodiments, L³ includes one or more substituents selected fromcarboxylic group, sulfonic acid group, ammonium, and amino group.

In certain embodiments of the compounds disclosed herein, thepolymerizable moiety is selected from —NH(CO)C(R)CH₂, —O(CO)C(R)CH₂, and—CHCH₂, wherein R is H or C₁-C₃ alkyl.

In some embodiments of the compounds disclosed herein, R¹³ is H, C₁-C₆alkyl, polymerizable moiety, or NIR dye moiety.

In other embodiments of the compounds disclosed herein, R¹³ is an NIRdye moiety.

Exemplary NIR dye moieties of the compounds disclosed herein areselected from cyanine, hemicyanine, fluorone, oxazine, phenanthridine,rhodamine, rosamine, indolium, quinolinium, benzophenoxazine,benzopyrillium, bisindoylmaleimide, boron-dipyrromethene,boron-aza-dipyrromethene, carbopyronins, perylene, porphyrin, rutheniumcomplex, lanthanide complex, benzoxanthenium, xanthene, fluorescein,squaraine, coumarin, anthracene, tetracene, pentacene, and pyrene dyes.

In some instances, the NIR dye moiety has the structure selected from:

-   -   wherein R^(N1) and R^(N2) are independently C₁-C₁₀ alkyl        optionally substituted with one or more sulfo or carboxylic acid        groups, and the wavy lines denote the point of attachment to L².

In other embodiments, the NIR dye moiety has the structure of:

-   -   wherein R′, at each occurrence, is independently H, optionally        substituted C₁-C₁₀ alkyl, optionally substituted C₂-C₁₀ alkenyl,        optionally substituted C₂-C₁₀ alkynyl, or optionally substituted        C₂-C₂₀ heteroalkyl.

In yet other embodiments, the NIR dye moiety has the structure of:

-   -   wherein Y¹ is selected from O, P(O)R′, SiR′R″, and NR′, wherein        R′ and R″ are independently H or C₁-C₆ alkyl;    -   R²⁰ and R²¹ are independently H, C₁-C₆ alkyl, or R²¹ and R²⁰,        together with the nitrogen atom to which they are attached, form        a form a 6- or 5-membered ring optionally substituted with a        polymerizable moiety;    -   R²³ and R²⁴ are independently H, C₁-C₆ alkyl, or R²³ and R²⁴,        together with the nitrogen atom to which they are attached, form        a form a 6- or 5-membered ring optionally substituted with a        polymerizable moiety;    -   R²² and R²⁵ are independently H, C₁-C₆ alkyl, or R²¹ and R²²,        together with the atoms to which they are attached, form a 6- or        5-membered ring, or R²⁴ and R²⁵, together with the atoms to        which they are attached, form a 6- or 5-membered ring; and    -   R²⁶ and R²⁷ are independently H, C₁-C₆ alkyl, or R²⁶ and R²⁰,        together with the atoms to which they are attached, form a 6- or        5-membered ring, or R²⁷ and R²³, together with the atoms to        which they are attached, form a 6- or 5-membered ring.

In certain embodiments, Y¹ is SiMe₂.

In some embodiments of the compounds disclosed herein, Z is anoptionally substituted phenylene or anthracenylene.

In some embodiments, the compounds have the structure of Formula II:

-   -   or an isomer, a tautomer, or a salt thereof,    -   wherein R¹, R², R³, R⁴, R⁵, R⁶, R⁷, R⁸, R⁹, R¹⁰, R¹¹, R¹², R¹³,        R¹⁴, R¹⁵, L¹, L² and L³ are as defined for compound of Formula        I, and wherein the compound includes one or more NIR dye        moieties and one or more polymerizable moieties.

In some embodiments, the compounds have the structure of Formula III:

-   -   wherein the dotted lines denote a bond or absence of a bond;    -   when the dotted line connecting R¹ and O is a bond, R¹ is CX¹X²        and R¹⁵ is absent; and when the dotted line connecting R¹ and O        is absence of a bond, R¹⁵, at each occurrence, is independently        H or C₁-C₆ alkyl, and R¹, at each occurrence, is H, optionally        substituted C₁-C₆ alkyl, optionally substituted C₂-C₆ alkenyl,        optionally substituted C₂-C₆ alkynyl, optionally substituted        C₂-C₁₀ heteroalkyl, polymerizable moiety, NIR dye moiety,        electron-withdrawing group, or electron-donating group;    -   X¹ and X² are independently H or C₁-C₆ alkyl;    -   R² is H or C₁-C₆ alkyl;    -   R³, R⁴, R⁵, R⁶, R⁷, R⁸, R¹¹, R¹², and R¹⁴ are independently H,        optionally substituted C₁-C₆ alkyl, optionally substituted C₂-C₆        alkenyl, optionally substituted C₂-C₆ alkynyl, optionally        substituted C₂-C₁₀ heteroalkyl, polymerizable moiety, NIR dye        moiety, electron withdrawing group, or electron donating group;    -   R⁹, R¹⁰, and R¹³ are independently H, optionally substituted        C₁-C₆ alkyl, optionally substituted C₂-C₆ alkenyl, optionally        substituted C₂-C₆ alkynyl, optionally substituted C₂-C₁₀        heteroalkyl, polymerizable moiety, or NIR dye;    -   L¹, L², and L³ are independently linker group or absent; and    -   wherein the compound includes one or more NIR dye moieties and        one or more polymerizable moieties.

In certain embodiments, the compounds have the structure of FormulaIIIF:

or an isomer, a tautomer, or a salt thereof,

wherein the dotted lines at each occurrence independently denote a bondor absence of a bond; and when the dotted line connecting R¹ and O is abond, R¹ is CX¹X² and R¹⁵ is absent; and when the dotted line connectingR¹ and O is absence of a bond, R¹⁵ is H or C₁-C₆ alkyl;

X¹ and X² are independently H or C₁-C₆ alkyl;

R² is H or C₁-C₆ alkyl;

R³, R⁴, R⁵, R⁶, R⁷, R⁸, R¹¹, R¹², and R¹⁴ are independently H, C₁-C₆alkyl, polymerizable moiety, electron-withdrawing group, orelectron-donating group;

R⁹ and R¹⁰ are independently H, C₁-C₆ alkyl, polymerizable moiety, orNIR dye;

L¹ and L³ are independently a bond or a linker group selected fromoptionally substituted C₁-C₁₀ alkyl, optionally substituted C₂-C₁₀alkenyl, optionally substituted C₂-C₁₀ alkynyl, optionally substitutedC₂-C₂₀ heteroalkyl;

L² is a bond, optionally substituted C₁-C₁₀ alkyl, optionallysubstituted C₂-C₁₀ alkenyl, optionally substituted C₂-C₁₀ alkynyl,optionally substituted C₂-C₂₀ heteroalkyl; —O—, optionally substituted—CH₂C₆H₄O—, amido, amino, optionally substituted C₆-C₁₀ arylene, oroptionally substituted C₅-C₁₀ heteroarylene;

-   -   Y¹ is selected from O, P(O)R′, SiR′R″, and NR′, wherein R′ and        R″ are independently H or C₁-C₆ alkyl;    -   R²⁰ and R²¹ are independently H, C₁-C₆ alkyl or R²¹ and R²⁰,        together with the nitrogen atom to which they are attached, form        a form a 6- or 5-membered ring optionally substituted with a        polymerizable moiety;    -   R²³ and R²⁴ are independently H, C₁-C₆ alkyl, or R²³ and R²⁴,        together with the nitrogen atom to which they are attached, form        a form a 6- or 5-membered ring optionally substituted with a        polymerizable moiety;    -   R²² and R²⁵ are independently H, C₁-C₆ alkyl, or R²¹ and R²²,        together with the atoms to which they are attached, form a 6- or        5-membered ring, or R²⁴ and R²⁵, together with the atoms to        which they are attached, form a 6- or 5-membered ring;    -   R²⁶ and R²⁷ are independently H, C₁-C₆ alkyl, or R²⁶ and R²⁰,        together with the atoms to which they are attached, form a 6- or        5-membered ring, or R²⁷ and R²³, together with the atoms to        which they are attached, form a 6- or 5-membered ring; and        the compound includes one or more polymerizable moieties.

In some embodiments, L² is a bond, optionally substituted phenylene,

or —C₆H₄—O—.

In certain embodiments, Y¹ is SiMe₂.

In some embodiments, R¹⁰ is NHC(O)C(CH₃)CH₂

In certain embodiments, R⁹ is NHC(O)C(CH₃)CH₂.

In some embodiments of the compounds disclosed herein, the NIR dyemoiety is a silicon rosamine dye moiety.

In certain embodiments, L¹ is optionally substituted C₁-C₁₀ alkyl oroptionally substituted C₂-C₂₀ heteroalkyl. In certain embodiments, L³ isoptionally substituted C₁-C₁₀ alkyl or optionally substituted C₂-C₂₀heteroalkyl.

In some embodiments, R¹¹, R¹⁴, and R¹² are H. In other embodiments, R²²,R²⁵, R²⁶, and R²⁷ are H.

In some embodiments, wherein both R¹⁵ are H, and R¹ at each occurrenceis independently selected from the group consisting of H; anelectron-withdrawing group selected from the group consisting ofhalogen, C(O)R′, COOR′, C(O)NH₂, NHC(O)R′, C(O)NR′R″, CF₃, CN, SO₃H,SO₂CF₃, SO₂R′, SO₂NR′R″, ammonium, alkyl ammonium, and NO₂, wherein R′and R″ are independently H or C₁-C₆ alkyl; and electron-donating groupselected from the group consisting of NR^(N1)R^(N2), OR′, NHC(O)R′,OC(O)R′, phenyl, and vinyl, wherein R^(N1), R^(N2), and R′ areindependently H or C₁-C₆ alkyl.

Another aspect relates to a polymer including, as a monomer repeat unit,the residue of a compound of Formulae I-IIIH The polymers providedherein can be luminescent biocompatible hydrogels.

A further aspect relates to various luminescent sensors including thepolymers provided herein for detecting an analyte, e.g., glucose, invivo or in vitro. The sensors can be in the form of a powder, fabric(e.g., bandage), needle, rod, disk, or any other suitable form.

In some embodiments, the luminescent sensors provided herein aretissue-integrating or include a tissue-integrating scaffold and producea detectable signal in the presence of the analyte, for example, thesensors provide detection of the analyte when placed (e.g., implanted)into a tissue of a subject. The tissue-integrating sensors as describedherein can provide long-term detection of the analyte(s).

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 depicts performance of a glucose sensor prepared byco-polymerization of an exemplary compound (compound 21) implanted inthe subcutaneous tissue of a pig.

FIG. 2 depicts long-term stability and performance of two glucosesensors prepared by co-polymerization of an exemplary compound (compound21) implanted in the subcutaneous tissue of a pig.

DETAILED DESCRIPTION OF THE INVENTION

Described herein are polymerizable luminescent dyes useful forincorporation into polymers and polymers including covalently attached,e.g., as monomeric units, residues of the dyes. The dyes and thepolymers are useful in sensing and imaging applications, for example, toprovide accurate and optionally long term measurements of glucose invivo.

Additionally, described herein are sensors including the polymersdescribed herein. The sensors can be implanted into a tissue of asubject and used for long-term or short-term continuous andsemi-continuous collection of data of various biochemical analytes,optionally without the use of implantable hardware of any type and/orenzymatic and electrochemical detection methods. In one aspect, thesensors are tissue integrating, e.g., allow capillaries to grow in closeproximity to all regions of the sensor (e.g., on the surface andinside), which results in accurate analyte measurements, including overlong term.

Advantages of the dyes and luminescent polymers provided herein include,but are not limited to: (1) excitation and emission wavelengths in theoptical window of the skin (approximately 550 nm to 1100 nm) allowingdetection of analytes deep within a tissue or an organ; (2) highsignal-to-noise ratio; (3) large Stokes shifts and emission; (4)photostablity, e.g., the dyes and/or polymers do not undergo rapidphotobleaching.

Advantages of the sensors described herein include, but are not limitedto: (1) providing devices that generate stable signal over a long periodof time (e.g., greater than a week, greater than 10 days, greater than15 days, greater than 20 days, greater than a month, greater than 2months, greater than 3 months, or greater than 6 months), (2) providingdevices that are placed or implanted and integrate into the subject'stissue (e.g., through tissue and/or capillary in-growth); (3) providingdevices which can be implanted through syringe injection or trocarinjection, meaning that no surgery is required to put the sensing mediain place in the body; (4) providing devices that do not include sensorelectronics in the body; (5) providing devices that accurately assessanalyte (e.g., glucose) concentration for long periods of time (e.g.,greater than a week, weeks, months, or years) and/or (6) providingdevices of small dimensions which will give result in increased patientcomfort and better acceptance by the body.

It must be noted that, as used in this specification and the appendedclaims, the singular forms “a”, “an”, and “the” include plural referentsunless the content clearly dictates otherwise. Thus, for example,reference to a sensor including “a sensing moiety” includes devicesincluding two or more sensing moieties. Likewise, reference to “ananalyte” refers to two or more analytes.

Definitions

The term “tissue integrating” refers to a material (e.g., scaffold)which, when integrated into living tissue remains in close proximitywith the blood vessels of the tissue (e.g., capillaries).

By “long-term” it is meant that the implant senses the analyte forgreater than about 7 days, greater than about four weeks, greater thanabout one or more weeks, greater than about six weeks, greater thanabout one or more months, greater than about 100 days, or greater thanabout one or more years.

By “biodegradable” or “bioabsorbable” it is meant that the material iscapable of being broken down by the subject's body over a period oftime, ranging from days to weeks to months or years.

By “hydrogel” it is meant a material that absorbs a solvent (e.g.water), undergoes rapid swelling without discernible dissolution, andmaintains three-dimensional networks capable of reversible deformation.

The term “stimuli-responsive” refers to substances, e.g., polymers, thatchange their physical state, e.g., undergo a phase transition, whenexposed to an external stimulus or according to the environment they arein. Non-limiting examples of such polymers are “smart polymers” (KumarA. et al., Smart polymers: Physical forms and bioengineeringapplications. Prog. Polym. Sci. 32 (2007) 1205-1237).

As used herein, an electron-withdrawing group or EWG is a moiety, e.g.,an atom or group, which draws electron density from the neighboringatoms towards itself, usually by resonance or inductive effects. Anelectron-donating group or EDG is a moiety, e.g., an atom or group,which releases electron density to the neighboring atoms from itself,usually by resonance or inductive effects. Non-limiting examples of EWGare halogen, C(O)R′, COOR′, C(O)NH₂, NHC(O)R′, C(O)NR′R″, CF₃, CN, SO₃H,SO₂CF₃, SO₂R′, SO₂NR′R″, alkyl ammonium, and NO₂, wherein R′ and R″ areindependently H or C₁-C₆ alkyl. Non-limiting examples of EDG areNR^(N1)R^(N2), OR′, NHC(O)R′, OC(O)R′, phenyl, and vinyl, whereinR^(N1), R^(N2), and R′ are independently H or C₁-C₆ alkyl.

As used herein, a “linker group” or a “linker” is an n-valent moietythat connects n other moieties within a molecule. Typically, a linkergroup is a divalent moiety connecting two other moieties within amolecule.

The term “acyl,” as used herein, refers to a group of the form —C(O)R,wherein R is H or an optionally substituted group selected from alkyl,alkenyl, alkynyl, heteroalkyl, heteroalkenyl, heteroalkynyl, aryl, andheteroaryl.

As used herein, the terms “alkyl,” “alkenyl,” and “alkynyl” includestraight-chain, branched-chain and cyclic monovalent hydrocarbylradicals, and combinations of these, which contain only C and H whenthey are unsubstituted. Examples include methyl, ethyl, isobutyl,cyclohexyl, cyclopentylethyl, 2-propenyl, 3-butynyl, and the like. Thetotal number of carbon atoms in each such group is sometimes describedherein, e.g., when the group can contain up to ten carbon atoms it canbe represented as 1-10C, C₁-C₁₀, C₁-C₁₀, or C1-10. The term“heteroalkyl,” “heteroalkenyl,” and “heteroalkynyl,” as used herein,mean the corresponding hydrocarbons wherein one or more chain carbonatoms have been replaced by a heteroatom. Exemplary heteroatoms includeN, O, S, and P. When heteroatoms are allowed to replace carbon atoms,for example, in heteroalkyl groups, the numbers describing the group,though still written as e.g. C1-C10, represent the sum of the number ofcarbon atoms in the cycle or chain plus the number of such heteroatomsthat are included as replacements for carbon atoms in the cycle or chainbeing described.

Alkyl, alkenyl, and alkynyl substituents may contain 1-10 carbon atoms(alkyl) or 2-10 carbon atoms (alkenyl or alkynyl). In an embodiment,they contain 1-8 carbon atoms (alkyl) or 2-8 carbon atoms (alkenyl oralkynyl). Sometimes they contain 1-6 carbon atoms (alkyl) or 2-6 carbonatoms (alkenyl or alkynyl). Sometimes they contain 1-4 carbon atoms(alkyl) or 2-4 carbon atoms (alkenyl or alkynyl). A single group caninclude more than one type of multiple bond, or more than one multiplebond; such groups are included within the definition of the term“alkenyl” when they contain at least one carbon-carbon double bond, andare included within the term “alkynyl” when they contain at least onecarbon-carbon triple bond.

Alkyl, alkenyl, and alkynyl groups can be optionally substituted to theextent that such substitution makes sense chemically. Substituentsinclude, but are not limited to, halogens (F, Cl, Br, I), ═O, ═N—CN,═N—OR, ═NR, OR, NR₂, SR, SO₂R, SO₂NR₂, NRSO₂R, NRCONR₂, NRC(O)OR,NRC(O)R, CN, C(O)OR, C(O)NR₂, OC(O)R, C(O)R, and NO₂, wherein each R isindependently H, C1-C8 alkyl, C2-C8 heteroalkyl, C1-C8 acyl, C2-C8heteroacyl, C2-C8 alkenyl, C2-C8 heteroalkenyl, C₂-C₈ alkynyl, C2-C8heteroalkynyl, C6-C10 aryl, or C5-C10 heteroaryl, and each R isoptionally substituted with halogens (F, Cl, Br, I), ═O, ═N—CN, ═N—OR′,═NR′, OR′, NR′2, SR′, SO₂R′, SO₂NR′₂, NR′SO₂R′, NR′CONR′₂, NR′C(O)OR′,NR′C(O)R′, CN, C(O)OR′, C(O)NR′₂, OC(O)R′, C(O)R′, and NO₂, wherein eachR′ is independently H, C1-C8 alkyl, C2-C8 heteroalkyl, C1-C8 acyl, C2-C8heteroacyl, C6-C10 aryl or C5-C10 heteroaryl. Alkyl, alkenyl and alkynylgroups can also be substituted by C1-C8 acyl, C2-C8 heteroacyl, C6-C10aryl or C5-C10 heteroaryl, each of which can be substituted by thesubstituents that are appropriate for the particular group.

While “alkyl” as used herein includes cycloalkyl and cycloalkylalkylgroups, the term “cycloalkyl” is used herein to describe a carbocyclicnon-aromatic group that is connected via a ring carbon atom, and“cycloalkylalkyl” is used to describe a carbocyclic non-aromatic groupthat is connected to the molecule through an alkyl linker. Similarly,“heterocyclyl” is used to identify a non-aromatic cyclic group thatcontains at least one heteroatom as a ring member and that is connectedto the molecule via a ring atom, which may be C or N; and“heterocyclylalkyl” may be used to describe such a group that isconnected to another molecule through an alkylene linker. As usedherein, these terms also include rings that contain a double bond ortwo, as long as the ring is not aromatic.

“Aromatic” or “aryl” substituent or moiety refers to a monocyclic, fusedbicyclic, a fused tricyclic, or a fused tetracyclic moiety having thewell-known characteristics of aromaticity; examples include phenyl,naphthyl, and anthracenyl. Similarly, “heteroaromatic” and “heteroaryl”refer to such aromatic ring systems which contain as ring members one ormore heteroatoms. Suitable heteroatoms include N, O, and S, inclusion ofwhich permits aromaticity in 5-membered rings as well as 6-memberedrings. Heteroaromatic systems include monocyclic C5-C6 heterorayls suchas pyridyl, pyrimidyl, pyrazinyl, thienyl, furanyl, pyrrolyl, pyrazolyl,thiazolyl, oxazolyl, and imidazolyl, and fused bicyclic moieties formedby fusing one of these monocyclic groups with a phenyl ring or with anyof the heteroaromatic monocyclic groups to form a C8-C10 bicyclic groupsuch as indolyl, benzimidazolyl, indazolyl, benzotriazolyl, isoquinolyl,quinolyl, benzothiazolyl, benzofuranyl, pyrazolopyridyl, quinazolinyl,quinoxalinyl, cinnolinyl, and the like. Any monocyclic or fused ringbicyclic system which has the characteristics of aromaticity in terms ofelectron distribution throughout the ring system is included in thisdefinition. It also includes bicyclic groups where at least the ringwhich is directly attached to the remainder of the molecule has thecharacteristics of aromaticity. Typically, monocyclic heteroarylscontain 5-6 ring members, and the bicyclic heteroaryls contain 8-10 ringmembers.

Aryl and heteroaryl moieties may be substituted with a variety ofsubstituents including C1-C8 alkyl, C2-C8 alkenyl, C2-C8 alkynyl, C5-C12aryl, C1-C8 acyl, and heteroforms of these, each of which can itself befurther substituted; other substituents for aryl and heteroaryl moietiesinclude halogens (F, Cl, Br, I), OR, NR₂, SR, SO₂R, SO₂NR₂, NRSO₂R,NRCONR₂, NRC(O)OR, NRC(O)R, CN, C(O)OR, C(O)NR₂, OC(O)R, C(O)R, and NO₂,wherein each R is independently H, C1-C8 alkyl, C2-C8 heteroalkyl, C2-C8alkenyl, C2-C8 heteroalkenyl, C2-C8 alkynyl, C2-C8 heteroalkynyl, C6-C10aryl, C5-C10 heteroaryl, C7-C12 arylalkyl, or C6-C12 heteroarylalkyl,and each R is optionally substituted as described above for alkylgroups. The substituent groups on an aryl or heteroaryl group may ofcourse be further substituted with the groups described herein assuitable for each type of such substituents or for each component of thesubstituent. Thus, for example, an arylalkyl substituent may besubstituted on the aryl portion with substituents described herein astypical for aryl groups, and it may be further substituted on the alkylportion with substituents described herein as typical or suitable foralkyl groups.

“Optionally substituted,” as used herein, indicates that the particulargroup being described may have one or more hydrogen substituentsreplaced by a non-hydrogen substituent. In some optionally substitutedgroups or moieties, all hydrogen substituents are replaced by anon-hydrogen substituent. If not otherwise specified, the total numberof such substituents that may be present is equal to the number of Hatoms present on the unsubstituted form of the group being described.Where an optional substituent is attached via a double bond, such as acarbonyl oxygen or oxo (═O), the group takes up two available valences,so the total number of substituents that may be included is reducedaccording to the number of available valences.

A. Luminescent Compounds Including a NIR Dye Moiety and One or MorePolymerizable Groups

One aspect relates to a compound of Formula I:

-   -   or an isomer, a tautomer, or a salt thereof, wherein the dotted        lines denote a bond or absence of a bond, and when the dotted        line connecting R¹ and O is a bond, R¹ is CX¹X² and R¹⁵ is        absent; and when the dotted line connecting R¹ and O is absence        of a bond, R¹⁵, at each occurrence, is independently H or C₁-C₆        alkyl, and R¹ at each occurrence, is selected from H, optionally        substituted C₁-C₆ alkyl, optionally substituted C₂-C₆ alkenyl,        optionally substituted C₂-C₆ alkynyl, optionally substituted        C₂-C₁₀ heteroalkyl, polymerizable moiety, NIR dye moiety,        electron-withdrawing group, and electron-donating group;    -   R² is H or C₁-C₆ alkyl;    -   Z is a C₆-C₁₄ arylene optionally substituted with R¹¹, R¹², R¹⁴,        and L²R¹³;    -   R³, R⁴, R⁵, R⁶, R, R⁸, R¹¹, R¹², R¹³, and R¹⁴ are independently        selected from H, C₁-C₆ alkyl, polymerizable moiety, NIR dye        moiety, electron withdrawing group, and electron donating group;    -   R⁹ and R¹⁰ are independently selected from H, C₁-C₆ alkyl,        polymerizable moiety, and NIR dye;    -   X¹ and X² are independently H, halogen, or C₁-C₆ alkyl;    -   L¹, L², and L³ are independently linker group or absent;    -   the dotted line denotes a bond or absence of a bond, and    -   wherein the compound includes one or more NIR dye moieties and        one or more polymerizable moieties.

In certain embodiments of Formula I, the compound has a structure ofFormula IA, IB, or IC:

-   -   or an isomer, a tautomer, or a salt thereof, wherein all        substituents are as defined above for Formula I.

In other embodiments of Formula I, IA, IB, or IC, the compound includes1 NIR dye moiety. In other embodiments of Formula I, IA, IB, or IC, thecompound includes 1 polymerizable moiety. In still other embodiments ofFormula I, IA, IB, or IC, the compound includes 2 polymerizablemoieties. In certain embodiments of Formula I, IA, IB, or IC, thepolymerizable moieties have the same structure. In other embodiments ofFormula I, IA, IB, or IC, the polymerizable moieties have differentstructures.

In some embodiments of Formula I, IA, IB, or IC, theelectron-withdrawing group is selected from the group consisting ofhalogen, C(O)R′, COOR′, C(O)NH₂, NHC(O)R′, C(O)NR′R″, CF₃, CN, SO₃H,SO₂CF₃, SO₂R′, SO₂NR′R″, ammonium, alkyl ammonium, and NO₂, and whereinR′ and R″ are independently H or C₁-C₆ alkyl.

In other embodiments of Formula I, IA, IB, or IC, the electron-donatinggroup is selected from the group consisting of NR^(N1)R^(N2), OR′,NHC(O)R′, OC(O)R′, phenyl, and vinyl, wherein R^(N1), R^(N2), and R′ areindependently H or C₁-C₆ alkyl.

In other embodiments of Formula I, IA, IB, or IC, L¹ is a linker groupselected from optionally substituted amino, optionally substitutedamido, —O—, optionally substituted C₁-C₆ alkylene, optionallysubstituted C₂-C₆ alkenylene, optionally substituted C₂-C₆ alkynylene,optionally substituted C₂-C₂₀ heteroalkylene, optionally substitutedC₆-C₁₀ arylene, optionally substituted C₂-C₁₀ heteroarylene, and acombination thereof.

In other embodiments of Formula I, IA, IB, or IC, L² is a linker groupselected from optionally substituted amino, optionally substitutedamido, —O—, optionally substituted C₁-C₆ alkylene, optionallysubstituted C₂-C₆ alkenylene, optionally substituted C₂-C₆ alkynylene,optionally substituted C₂-C₂₀ heteroalkylene, optionally substitutedC₆-C₁₀ arylene, optionally substituted C₂-C₁₀ heteroarylene, and acombination thereof.

In certain embodiments of Formula I, IA, IB, or IC, L³ is a linker groupselected from optionally substituted amino, optionally substitutedamido, —O—, optionally substituted C₁-C₆ alkylene, optionallysubstituted C₂-C₆ alkenylene, optionally substituted C₂-C₆ alkynylene,optionally substituted C₂-C₂₀ heteroalkylene, optionally substitutedC₆-C₁₀ arylene, optionally substituted C₂-C₁₀ heteroarylene, and acombination thereof.

In other embodiments of Formula I, IA, IB, or IC, L¹, L², and L³ areindependently optionally substituted with one or more groups selectedfrom carboxylic group, sulfonic acid group, ammonium, amino group, and acombination thereof.

In still other embodiments of Formula I, IA, IB, or IC, L¹, L², and L³independently include one or more substituents selected from carboxylicgroup, sulfonic acid group, ammonium, and amino group.

In some embodiments of Formula I, IA, IB, or IC, L¹, L², and L³ areindependently optionally substituted —C₁-C₆ alkylene-Ar—, optionallysubstituted C₂-C₆ alkenylene-Ar—, optionally substituted C₂-C₆alkynylene-Ar—, optionally substituted —C(O)NH—C₁-C₆ alkylene-Ar—,optionally substituted —C1-C6 alkylene-C(O)NH—C₁-C₆ alkylene-Ar—,—(CH₂CH₂O)_(n)—, wherein n is an integer between 1 and 10 and Ar is anoptionally substituted phenylene or an optionally substituted 5-memberedheteroarylene. In some of the above embodiments, the one or more of thelinker groups is optionally substituted with one or more groups selectedfrom carboxylic group, sulfonic acid group, ammonium, amino group, and acombination thereof.

In particular embodiments of Formula I, IA, IB, or IC, the one or morepolymerizable moiety includes a group selected from —NH(CO)C(R)CH₂,—O(CO)C(R)CH₂, and —CHCH₂, wherein R is H or C₁-C₃ alkyl. In certainembodiments of Formula I, IA, IB, or IC, the one or more polymerizablemoiety is selected from —NH(CO)C(R)CH₂, —O(CO)C(R)CH₂, and —CHCH₂,wherein R is H or C₁-C₃ alkyl.

In some embodiments of Formula I, IA, IB, or IC, R¹³ is H, C₁-C₆ alkyl,polymerizable moiety, or NIR dye moiety.

In other embodiments of Formula I, IA, IB, or IC, R¹³ is an NIR dyemoiety.

In some embodiments of Formula I, IA, IB, or IC, the one or more NIR dyemoiety is cyanine, hemicyanine, fluorone, oxazine, phenanthridine,rhodamine, rosamine, indolium, quinolinium, benzophenoxazine,benzopyrillium, bisindoylmaleimide, boron-dipyrromethene,boron-aza-dipyrromethene, carbopyronins, perylene, porphyrin, rutheniumcomplex, lanthanide complex, benzoxanthenium, xanthene, fluorescein,squaraine, coumarin, anthracene, tetracene, pentacene, or pyrene dyeresidue.

In certain embodiments of Formula I, IA, IB, or IC, the NIR dye hasexcitation and emission wavelengths in the optical window of the skin.In other embodiments of Formula I, IA, IB, or IC, NIR dye has anabsorbtion maximum between about 500 nm and about 900 nm, between about600 nm and about 1000 nm, and between about 500 nm and about 1000 nm. Inyet other embodiments of Formula I, IA, IB, or IC, the NIR dye has anemission maximum between about 550 nm and about 900 nm, between about600 nm and about 1000 nm, and between about 550 nm and about 1100 nm. Incertain embodiments of Formula I, IA, IB, or IC, the compound itself isa NIR dye and has an absorbtion maximum between about 550 nm and about1000 nm and an emission maximum between about 600 nm and about 1100 nm.an absorption maximum greater than 500 nm, greater than 550 nm, greaterthan 600 nm, greater than 650 nm, greater than 700 nm. In certainembodiments of Formula I, IA, IB, or IC, the compound itself is a NIRdye and has an absorption maximum greater than 500 nm, greater than 550nm, greater than 600 nm, greater than 650 nm, greater than 700 nm. Inother embodiments of Formula I, IA, IB, or IC, the compound itself is aNIR dye and has an emission maximum greater than 550 nm, greater than600 nm, greater than 650 nm, greater than 700 nm, greater than 800 nm,greater than 900 nm, greater than 1000 nm, greater than 1100 nm.

In particular embodiments of Formula I, IA, IB, or IC, Z is anoptionally substituted phenylene.

In other embodiments of Formula I, IA, IB, or IC, compound has thestructure of Formula II:

-   -   or an isomer, a tautomer, or a salt thereof,    -   wherein R¹, R², R³, R⁴, R⁵, R⁶, R⁷, R⁸, R⁹, R¹⁰, R¹¹, R¹², R¹³,        R¹⁴, R¹⁵, L¹, L² and L³ are as defined for compound of Formula        I, IA, IB, or IC, and wherein the compound includes one or more        NIR dye moieties and one or more polymerizable moieties.

In other embodiments of Formula II, R³, R⁵, R⁶, and R⁸ are H.

In some embodiments of Formula II, the compound has a structure ofFormula IIA:

In certain embodiments of Formula II or IIA, L² is absent and R¹³ is H.In other embodiments of Formula II or IIA, R⁴, R⁷, R¹¹, R¹², and R¹⁴ areH. In yet other embodiments of Formula II or IIA, L³ is optionallysubstituted C₁-C₆ alkylene. In particular embodiments of Formula II orIIA, R⁹ is —NHC(O)CH₃CH₂.

In certain embodiments of Formula II or IIA, the dotted line between R¹and O is absence of a bond, R¹⁵ is absent, and R¹ and R² are H.

In some embodiments of Formula II or IIA, R¹³ is H, C₁-C₆ alkyl,polymerizable moiety, or NIR dye moiety.

In other embodiments of Formula II or IIA, R¹³ is an NIR dye moiety.

In certain embodiments of Formula II or IIA, the compound has astructure of Formula IIB:

In some embodiments of Formula II, IIA, or IIB, the compound is selectedfrom compounds 1, 2, 3, 4, 5, 6, or 7 of Table 1.

In certain embodiments of Formula I, IA, IB, or IC, the compound has astructure of Formula III:

-   -   or an isomer, a tautomer, or a salt thereof,    -   wherein the dotted lines denote a bond or absence of a bond;    -   when the dotted line connecting R¹ and O is a bond, R¹ is CX¹X²        and R¹⁵ is absent; and when the dotted line connecting R¹ and O        is absence of a bond, R¹⁵, at each occurrence, is independently        H or C₁-C₆ alkyl, and R¹, at each occurrence, is selected from        independently H, C₁-C₆ alkyl, polymerizable moiety, NIR dye        moiety, electron withdrawing group, or electron donating group;    -   X¹ and X² are independently H or C₁-C₆ alkyl;    -   R² is H or C₁-C₆ alkyl;    -   Z is a C₆-C₁₄ arylene optionally substituted with R¹¹, R¹², R¹⁴,        and L²R¹³;    -   R³, R⁴, R⁵, R⁶, R⁷, R⁸, R¹¹, R¹², R¹³, and R¹⁴ are independently        H, C₁-C₆ alkyl, polymerizable moiety, NIR dye moiety,        electron-withdrawing group, or electron-donating group;    -   R⁹ and R¹⁰ are independently H, C₁-C₆ alkyl, polymerizable        moiety, or NIR dye;    -   L¹, L², and L³ are independently linker group or absent;    -   the dotted line denotes a bond or absence of a bond, and    -   wherein the compound includes one or more NIR dye moieties and        one or more polymerizable moieties.

In particular embodiments of Formula III, the electron-withdrawing groupis selected from the group consisting of halogen, C(O)R′, COOR′,C(O)NH₂, NHC(O)R′, C(O)NR′R″, CF₃, CN, SO₃H, SO₂CF₃, SO₂R′, ammonium,alkyl ammonium, and NO₂, and wherein R′ and R″ are independently H orC₁-C₆ alkyl. In other embodiments of Formula III, electron-donatinggroup is selected from the group consisting of NR^(N1)R^(N2) OR′,NHC(O)R′, OC(O)R′, phenyl, and vinyl, wherein R^(N1), R^(N2), and R′ areindependently H or C₁-C₆ alkyl. In yet other embodiments of Formula III,L¹ is a linker group selected from optionally substituted amino,optionally substituted amido, —O—, optionally substituted C₁-C₆alkylene, optionally substituted C₂-C₆ alkenylene, optionallysubstituted C₂-C₆ alkynylene, optionally substituted C₂-C₂₀heteroalkylene, C₆-C₁₀ arylene, optionally substituted C₂-C₁₀heteroarylene, and a combination thereof. In certain embodiments ofFormula III, wherein L² is a linker group selected from optionallysubstituted amino, optionally substituted amido, —O—, optionallysubstituted C₁-C₆ alkylene, optionally substituted C₂-C₆ alkenylene,optionally substituted C₂-C₆ alkynylene, optionally substituted C₂-C₂₀heteroalkylene, C₆-C₁₀ arylene, optionally substituted C₂-C₁₀heteroarylene, and a combination thereof. In some embodiments of FormulaIII, L³ is a linker group selected from optionally substituted amino,optionally substituted amido, —O—, optionally substituted C₁-C₆alkylene, optionally substituted C₂-C₆ alkenylene, optionallysubstituted C₂-C₆ alkynylene, optionally substituted C₂-C₂₀heteroalkylene, C₆-C₁₀ arylene, optionally substituted C₂-C₁₀heteroarylene, and a combination thereof. In certain embodiments ofFormula III, the linker group includes a substituent selected fromcarboxylic group, sulfonic acid group, ammonium, and amino group. Incertain embodiments of Formula III, the polymerizable moiety is selectedfrom —NH(CO)C(R)CH₂, —O(CO)C(R)CH₂, and —CHCH₂, wherein R is H or C₁-C₃alkyl.

In some embodiments of Formula III, the NIR dye moiety is cyanine,hemicyanine, fluorone, oxazine, phenanthridine, rhodamine, rosamine,indolium, quinolinium, benzophenoxazine, benzopyrillium,bisindoylmaleimide, boron-dipyrromethene, boron-aza-dipyrromethene,carbopyronins, perylene, porphyrin, ruthenium complex, lanthanidecomplex, benzoxanthenium, xanthene, fluorescein, squaraine, coumarin,anthracene, tetracene, pentacene, or pyrene dye residues.

In some embodiments of Formula III, R¹³ is H, C₁-C₆ alkyl, polymerizablemoiety, or NIR dye moiety.

In other embodiments of Formula III, R¹³ is an NIR dye moiety.

In other embodiments of Formula III, the NIR dye moiety has excitationand emission wavelengths in the optical window of the skin. Inparticular embodiments of Formula III, the NIR dye moiety has anabsorbtion maximum between about 500 nm and about 900 nm, between about600 nm and about 1000 nm, and between about 500 nm and about 1000 nm. Inother embodiments of Formula III, the NIR dye has an emission maximumbetween about 550 nm and about 900 nm, between about 600 nm and about1000 nm, and between about 550 nm and about 1100 nm. In certainembodiments of Formula III, compound itself is a NIR luminescent dye andhas an absorbtion maximum between about 550 nm and about 1000 nm and anemission maximum between about 600 nm and about 1100 nm. an absorptionmaximum greater than 500 nm, greater than 550 nm, greater than 600 nm,greater than 650 nm, greater than 700 nm. In other embodiments ofFormula III, the compound has an absorption maximum greater than 500 nm,greater than 550 nm, greater than 600 nm, greater than 650 nm, greaterthan 700 nm. In yet other embodiments of Formula III, the compound hasan emission maximum greater than 550 nm, greater than 600 nm, greaterthan 650 nm, greater than 700 nm, greater than 800 nm, greater than 900nm, greater than 1000 nm, greater than 1100 nm

In certain embodiments of Formula III, R³, R⁵, R⁶, and R⁸ are H.

In certain embodiments of Formula III, the compound has a structure ofFormula IIIA:

-   -   or an isomer, a tautomer, or a salt thereof.

In certain embodiments of Formula III or IIIA, L² is absent and R¹³ isH. In other embodiments of Formula III or IIIA, R⁴, R⁷, R¹¹, R¹², andR¹⁴ are H. In some embodiments of Formula III or IIIA, L³ is optionallysubstituted C₁-C₆ alkylene. In still other embodiments of Formula III orIIIA, R⁹ is —NHC(O)C(CH₃)CH₂. In certain embodiments of Formula III orIIIA, the dotted line connecting R¹ and O denotes absence of a bond andR¹ and R² are H.

In some embodiments of Formula IIIA, R¹³ is H, C₁-C₆ alkyl,polymerizable moiety, or NIR dye moiety.

In other embodiments of Formula IIIA, R¹³ is an NIR dye moiety.

In certain embodiments of Formula III or IIIA, the compound has astructure of Formula IIIB:

-   -   or an isomer, a tautomer, or a salt thereof.

In certain embodiments of Formula IIIB, the compound is selected fromcompounds 8, 9, 10, 11, 12, or 13 of Table 1.

In certain embodiments of Formula III, the compound has a structure ofFormula IIIC:

-   -   or an isomer, a tautomer, or a salt thereof.

In some embodiments of Formula IIIC, R¹³ is H, C₁-C₆ alkyl,polymerizable moiety, or NIR dye moiety.

In other embodiments of Formula IIIC, R¹³ is an NIR dye moiety.

In some embodiments of Formula III or IIIC, L² is —CHCH— and R¹³ is aNIR dye moiety. In other embodiments of Formula III or IIIC, R⁴ and R⁷are H.

In some embodiments of Formula IIIC, the compound is compound 14, 15,16, 17, or 18 of Table 1.

In certain embodiments of Formula III, the compound has a structure ofFormula IIID:

-   -   or an isomer, a tautomer, or a salt thereof,    -   wherein    -   the dotted line connecting R¹ and O is a bond or absence of a        bond;    -   R¹ is H or CX¹X²;    -   R¹⁵ is H or absent;    -   X¹ and X² are independently H or C₁-C₆ alkyl;    -   L¹, L², and L³ are linker moieties independently selected from a        bond, optionally substituted C₁-C₁₀ alkyl, optionally        substituted C₂-C₁₀ alkenyl, optionally substituted C₂-C₁₀        alkynyl, optionally substituted C₂-C₂₀ heteroalkyl; —CH₂C₆H₄O—,        C₂-C₂₀ PEG linker, amido, amino, and phenylene;    -   R³, R⁴, and R⁷ are independently H, C₁-C₆ alkyl,        electron-withdrawing group, or electron-donating group;    -   R¹³ is a NIR dye moiety; and    -   R¹⁰ and R⁹ are H or polymerizable moiety.

In some embodiments of Formula III or IIID, L¹ and L² are independentlyC₁-C₆ alkylene. In other embodiments of Formula III or IIID, R¹⁰ and R⁹are NHC(O)C(CH₃)CH₂. In yet other embodiments of Formula III or IIID,R³, R⁴, and R¹⁴ are H. In certain embodiments of Formula III or IIID,the compound is compound 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30,31, 32, 33, 34, or 35 of Table 1.

In certain embodiments of Formula III, the compound has a structure ofFormula IIIE:

-   -   or an isomer, a tautomer, or a salt thereof,    -   wherein    -   the dotted line connecting R¹ and O is a bond or absence of a        bond;    -   R¹ is H or CX¹X²;    -   R¹⁵ is H or absent;    -   X¹ and X² are independently H or C₁-C₆ alkyl;    -   L¹ and L³ are linker moieties independently selected from a        bond, optionally substituted C₁-C₆ alkylene, optionally        substituted C₂-C₆ alkenylene, optionally substituted C₂-C₆        alkynylene, —O—, optionally substituted C₂-C₂₀ PEG linker,        optionally substituted amido, optionally substituted amino, and        optionally substituted C₆-C₁₀ arylene;    -   R³, R⁴, and R⁷ are independently selected from H, C₁-C₆ alkyl,        electron-withdrawing group, and electron-donating group;    -   R¹³ is a NIR dye moiety; and    -   R¹⁰ and R⁹ are H or polymerizable moiety.

In particular embodiments of Formula IIIE, R¹⁰ and R⁹ areNHC(O)C(CH₃)CH₂.

In specific embodiments of Formula IIIE, the compound is compound 36,37, 38, 39, 40, or 41 of Table 1.

In certain embodiments of Formula III, the compound has a structure ofFormula IIIF:

or an isomer, a tautomer, or a salt thereof,

wherein the dotted lines independently denote a bond or absence of abond; and when the dotted line connecting R¹ and O is a bond, R¹ isCX¹X² and R¹⁵ is absent; and when the dotted line connecting R¹ and O isabsence of a bond, R¹⁵ is H or C₁-C₆ alkyl;

X¹ and X² are independently H or C₁-C₆ alkyl;

R² is H or C₁-C₆ alkyl;

R³, R⁴, R⁵, R⁶, R⁷, R⁸, R¹¹, R¹², and R¹⁴ are independently H, C₁-C₆alkyl, polymerizable moiety, electron-withdrawing group, orelectron-donating group;

R⁹ and R¹⁰ are independently H, C₁-C₆ alkyl, polymerizable moiety, orNIR dye;

L¹ and L³ are independently a bond or a linker group selected fromoptionally substituted C₁-C₁₀ alkyl, optionally substituted C₂-C₁₀alkenyl, optionally substituted C₂-C₁₀ alkynyl, optionally substitutedC₂-C₂₀ heteroalkyl;

L² is a bond, optionally substituted C₁-C₁₀ alkyl, optionallysubstituted C₂-C₁₀ alkenyl, optionally substituted C₂-C₁₀ alkynyl,optionally substituted C₂-C₂₀ heteroalkyl; —O—, optionally substituted—CH₂C₆H₄O—, C₂-C₂₀ PEG linker, amido, amino, optionally substitutedC₆-C₁₀ arylene, or optionally substituted C₅-C₁₀ heteroarylene;

-   -   A- is a counterion;    -   Y¹ is selected from O, P(O)R′, SiR′R″, and NR′, wherein R′ and        R″ are independently H or C₁-C₆ alkyl;    -   R²⁰ and R²¹ are independently H, C₁-C₆ alkyl or R²¹ and R²⁰,        together with the nitrogen atom to which they are attached, form        a form a 6- or 5-membered ring optionally substituted with a        polymerizable moiety;    -   R²³ and R²⁴ are independently H, C₁-C₆ alkyl, or R²³ and R²⁴,        together with the nitrogen atom to which they are attached, form        a form a 6- or 5-membered ring optionally substituted with a        polymerizable moiety;    -   R²² and R²⁵ are independently H, C₁-C₆ alkyl, or R²¹ and R²²,        together with the atoms to which they are attached, form a 6- or        5-membered ring, or R²⁴ and R²⁵, together with the atoms to        which they are attached, form a 6- or 5-membered ring;    -   R²⁶ and R²⁷ are independently H, C₁-C₆ alkyl, or R²⁶ and R²⁰,        together with the atoms to which they are attached, form a 6- or        5-membered ring, or R²⁷ and R²³, together with the atoms to        which they are attached, form a 6- or 5-membered ring; and    -   the compound includes one or more polymerizable moieties.

In some embodiments of Formula IIIF, the compound is compound 42-77, 81,82, 83, 84, 85, 86, 87, or 88 of Table 1.

In certain embodiments of Formula III, the compound has a structure ofFormula IIIG:

or an isomer, a tautomer, or a salt thereof,

wherein the dotted lines independently denote a bond or absence of abond; and when the dotted line connecting R¹ and O is a bond, R¹ isCX¹X² and R¹⁵ is absent; and when the dotted line connecting R¹ and O isabsence of a bond, R¹⁵ is H or C₁-C₆ alkyl;

X¹ and X² are independently H or C₁-C₆ alkyl;

R² is H or C₁-C₆ alkyl;

R³, R⁴, R⁵, R⁶, R⁷, R⁸, R¹¹, R¹², and R¹⁴ are independently H, C₁-C₆alkyl, polymerizable moiety, electron-withdrawing group, orelectron-donating group;

R⁹ and R¹⁰ are independently H, C₁-C₆ alkyl, polymerizable moiety, orNIR dye;

L¹ and L³ are independently a bond or a linker group selected fromoptionally substituted C₁-C₁₀ alkyl, optionally substituted C₂-C₁₀alkenyl, optionally substituted C₂-C₁₀ alkynyl, optionally substitutedC₂-C₂₀ heteroalkyl;

L² is a bond, optionally substituted C₁-C₁₀ alkyl, optionallysubstituted C₂-C₁₀ alkenyl, optionally substituted C₂-C₁₀ alkynyl,optionally substituted C₂-C₂₀ heteroalkyl; —O—, optionally substituted—CH₂C₆H₄O—, C₂-C₂₀ PEG linker, amido, amino, optionally substitutedC₆-C₁₀ arylene, or optionally substituted C₅-C₁₀ heteroarylene;

R′, at each occurrence, is independently H, optionally substitutedC₁-C₁₀ alkyl, optionally substituted C₂-C₁₀ alkenyl, optionallysubstituted C₂-C₁₀ alkynyl, or optionally substituted C₂-C₂₀heteroalkyl; and

wherein the compound includes one or more polymerizable moieties.

In certain embodiments of Formula III, the compound has a structure ofFormula IIIH:

or an isomer, a tautomer, or a salt thereof,

wherein the dotted lines independently denote a bond or absence of abond; and when the dotted line connecting R¹ and O is a bond, R¹ isCX¹X² and R¹⁵ is absent; and when the dotted line connecting R¹ and O isabsence of a bond, R¹⁵ is H or C₁-C₆ alkyl;

X¹ and X² are independently H or C₁-C₆ alkyl;

R² is H or C₁-C₆ alkyl;

R³, R⁴, R⁵, R⁶, R⁷, R⁸, R¹¹, R¹², and R¹⁴ are independently H, C₁-C₆alkyl, polymerizable moiety, electron-withdrawing group, orelectron-donating group;

R⁹ and R¹⁰ are independently H, C₁-C₆ alkyl, polymerizable moiety, orNIR dye;

L¹ and L³ are independently a bond or a linker group selected fromoptionally substituted C₁-C₁₀ alkyl, optionally substituted C₂-C₁₀alkenyl, optionally substituted C₂-C₁₀alkynyl, optionally substitutedC₂-C₂₀ heteroalkyl;

-   -   L² is a bond, optionally substituted C₁-C₁₀ alkyl, optionally        substituted C₂-C₁₀ alkenyl, optionally substituted C₂-C₁₀        alkynyl, optionally substituted C₂-C₂₀ heteroalkyl; —O—,        optionally substituted —CH₂C₆H₄O—, C₂-C₂₀ PEG linker, amido,        amino, optionally substituted C₆-C₁₀ arylene, or optionally        substituted C₆-C₁₀ heteroarylene;    -   R¹³ is an optionally substituted dye moiety selected from:

-   -   wherein R^(N1) and R^(N2) are independently H or C₁-C₁₀ alkyl        optionally substituted with one or more sulfo or carboxylic acid        groups, and the wavy line denotes the point of attachment to L².

In some embodiments of Formula IIIF-IIIH, L² is a bond, optionallysubstituted phenylene,

or —C₆H₄—O—.

In some embodiments of the compounds of Formula IIIF-IIIH, R¹⁰ isNHC(O)C(CH₃)CH₂

In certain embodiments of the compounds of Formula IIIF-IIIH, R⁹ isNHC(O)C(CH₃)CH₂.

In some embodiments of the compounds of Formula IIIF-IIIH, the NIR dyemoiety is a silicon rosamine dye moiety. In certain embodiments of thecompounds of Formula IIIF-IIIH, Y¹ is SiMe₂.

In certain embodiments of the compounds of Formula IIIF-IIIH, L¹ isoptionally substituted C₁-C₁₀ alkyl or optionally substituted C₂-C₂₀heteroalkyl. In certain embodiments, L³ is optionally substituted C₁-C₁₀alkyl or optionally substituted C₂-C₂₀ heteroalkyl.

In some embodiments of the compounds of Formula IIIF-IIIH, R¹¹, R¹⁴, andR¹² are H. In certain embodiments of the compounds of Formula IIIF, R²²,R²⁵, R²⁶, and R²⁷ are H.

In some embodiments, wherein both R¹⁵ are H, and R¹ at each occurrenceis independently selected from the group consisting of H; anelectron-withdrawing group selected from the group consisting ofhalogen, C(O)R′, COOR′, C(O)NH₂, NHC(O)R′, C(O)NR′R″, CF₃, CN, SO₃H,SO₂CF₃, SO₂R′, SO₂NR′R″, ammonium, alkyl ammonium, and NO₂, wherein R′and R″ are independently H or C₁-C₆ alkyl; and electron-donating groupselected from the group consisting of NR^(N1)R^(N2), OR′, NHC(O)R′,OC(O)R′, phenyl, and vinyl, wherein R^(N1), R^(N2), and R′ areindependently H or C₁-C₆ alkyl.

In one embodiment, the compounds of Formulae I-IIIH are near-IRluminescent dyes. In one embodiment, the compounds of Formulae I-IIIHhave an absorption maximum between about 500 nm and about 1000 nm,between about 550 nm and about 700 nm, between about 550 nm and about800 nm, between about 550 nm and about 900 nm, between about 600 nm andabout 800 nm, between about 600 nm and about 900 nm, or between about600 nm and about 1000 nm. In some embodiments, the compounds of FormulaeI-IIIH have an emission maximum between 550 and 1100 nm, between about600 nm and about 1100 nm, between about 700 nm and about 1100 nm,between about 600 nm and about 900 nm, between about 600 nm and about800 nm, or between about 600 nm and about 1000 nm. In one embodiment,the compounds of Formulae I-IIIH are photostable and have excitation andemission spectra in the NIR optical window of the skin.

In certain embodiments, the compounds of Formulae I-IIIH have anabsorption maximum greater than 500 nm, greater than 550 nm, greaterthan 600 nm, greater than 650 nm, greater than 700 nm. In otherembodiments, the compounds of Formulae I-IIIH have an emission maximumgreater than 550 nm, greater than 600 nm, greater than 650 nm, greaterthan 700 nm, greater than 800 nm, greater than 900 nm, greater than 1000nm, greater than 1100 nm.

In some embodiments, the dyes are encapsulated into a solid,oxygen-impermeable nanosphere. The nanospheres can be used forluminescent, non-oxygen sensitive applications.

The compounds may be synthesized using techniques known in the art.Synthesis of non-limiting examples of the compounds is described indetail below.

B. Polymers

The fluorescent dyes include polymerizable moietys, e.g., residue ofacrylic or methacrylic acid, and can be co-polymerized with othermonomers to provide polymers including near-IR luminescent groups. Whenthe compounds have 2 or more polymerizable moietys, the polymersobtained from their co-polymerization with other monomers can becrosslinked. Alternatively, another crosslinking monomer can be addedinto the polymerization mixture to achieve a higher degree ofcrosslinking of the resulting polymer.

Polymers described herein can be prepared in any suitable manner.Suitable synthetic methods used to produce the polymers provided hereininclude, by way of non-limiting examples, cationic, anionic, and freeradical polymerization. In certain embodiments, polymer synthesis isperformed neat or in any suitable solvent. Suitable solvents include,but are not limited to, pentane, hexane, dichloromethane, chloroform,water, ethylene glycol, propylene glycol, DMSO or dimethyl formamide(DMF). In certain embodiments, the polymer synthesis is performed at anysuitable reaction temperature, including, e.g., from about −50° C. toabout 100° C., or from about 0° C. to about 70° C.

In an embodiment, the polymers are prepared by the means of a freeradical polymerization. When a free radical polymerization process isused, (i) the monomer, (ii) optionally, the co-monomer(s), and (iii) anoptional source of free radicals are provided to trigger a free radicalpolymerization process. In some embodiments, the source of free radicalsis optional because some monomers may self-initiate upon heating at hightemperature. In certain instances, after forming the polymerizationmixture, the mixture is subjected to polymerization conditions. Suchconditions are optionally varied to any suitable level and include, byway of non-limiting example, temperature, pressure, light, atmosphere,ratios of starting components used in the polymerization mixture andreaction time. The polymerization is carried out in any suitable manner,including, e.g., in solution, dispersion, suspension, emulsion or bulk.

In some embodiments, initiators are present in the reaction mixture. Anysuitable initiator is optionally utilized if useful in thepolymerization processes described herein. Such initiators include, byway of non-limiting example, one or more of alkyl peroxides, substitutedalkyl peroxides, aryl peroxides, substituted aryl peroxides, acylperoxides, alkyl hydroperoxides, substituted alkyl hydroperoxides, arylhydroperoxides, substituted aryl hydroperoxides, heteroalkyl peroxides,substituted heteroalkyl peroxides, heteroalkyl hydroperoxides,substituted heteroalkyl hydroperoxides, heteroaryl peroxides,substituted heteroaryl peroxides, heteroaryl hydroperoxides, substitutedheteroaryl hydroperoxides, alkyl peresters, substituted alkyl peresters,aryl peresters, substituted aryl peresters, or azo compounds. Inspecific embodiments, benzoylperoxide (BPO) and/or AIBN are used asinitiators.

In some embodiments, polymerization processes are carried out in acontrolled (living) mode. Non-limiting examples of controlled (living)polymerization processes include reversible addition-fragmentation chaintransfer (RAFT) polymerization processes and Atom Transfer RadicalPolymerization (ATRP).

In certain embodiments, the polymer may be a hydrogel. For example, thehydrogel can be prepared by reacting hydroxyethyl methacrylate (HEMA),to form poly(hydroxyethyl methacrylate), pHEMA. Furthermore, variouscomonomers can be used in combination to alter the hydrophilicity,mechanical and swelling properties of the hydrogel (e.g. PEG, NVP, MAA).Non-limiting examples of polymers include 2-hydroxyethyl methacrylate,polyacrylamide, N-vinylpyrrolidone, N,N-dimethylacrylamide,poly(ethylene glycol) monomethacrylate (of varying molecular weights),diethylene glycol methacrylate, N-(2-hydroxypropyl)methacrylamide,glycerol monomethacrylate, 2,3-dihydroxypropyl methacrylate andcombinations thereof. Non-limiting examples of cross-linkers includetetraethylene glycol dimethacrylate, poly(ethylene glycol)(n)diacrylate(of varying molecular weights), ethoxylated trimethylolpropanetriacrylate, bisacrylamide, and combinations thereof. Non-limitingexamples of initiators include Ingacure Series (UV),Azobisisobutyronitrile (AIBN) (thermal), Ammonium Persulfate (APS)(thermal).

In one embodiment, the polymer is a luminescent hydrogel prepared byco-polymerization of HEMA and compound of Formulae I-IIIH.

In an exemplary embodiment, the polymer is prepared by co-polymerizationof DMA (N,N-dimethylacrylamide), AAm (acrylamide), PEGDAAm(poly-ethylene glycol diacrylamide), and a compound of Formulae I-IIIHin the presence of2,2′-azobis[2-(2-imidazolin-2-yl)propane]dihydrochloride in a suitablesolvent, e.g., a mixture of DMSO and water.

In another exemplary embodiment, the polymer is prepared byco-polymerization of AETACI ([2-(acryloyloxy)ethyl]trimethylammoniumchloride), PEGDAAm (poly-ethylene glycol diacrylamide), a compound ofFormulae I-IIIH in the presence of2,2′-azobis[2-(2-imidazolin-2-yl)propane]dihydrochloride in a suitablesolvent, e.g., a mixture of DMSO and water.

In yet other exemplary embodiment, the polymer is prepared byco-polymerization of HEMA (2-hydroxyethyl methacrylate) (44.1 uL), DMA(N,N-dimethylacrylamide) (29.4 uL), PEGDAAm (poly-ethylene glycoldiacrylamide), a compound of Formulae I-IIIH in the presence of2,2′-azobis[2-(2-imidazolin-2-yl)propane]dihydrochloride in a suitablesolvent, e.g., a mixture of DMSO and water.

The polymer may be degradable, either by the body (biodegradable) or bythe application of an external initiator to start or speed up thedegradation process (e.g. UV, ultrasonics, radio frequency, temperature,or other exogenous sources to initiate degradation.). For example, thepolymer may be biodegradable or bioresorbable or may include anybiodegradable or bioresorbable segments, including but not limited todegradable forms of alginates, poly(lactic acid), poly(vinyl alcohol),polyanhydrides, poly(glycolic acid), microporous polyesters, microporouspolyethers and cross-linked collagen. One specific example isUV-photopolymerization of poly(ethylene glycol)-diacrylate and acrylatedprotease-degradable peptides and VEGF as described by Phelps, et al(2010) Proc. Nat'l. Acad. Sci. USA 107 (8):3323-3328

In one embodiment, polymers provided herein are biocompatible. Inanother aspect, the polymers are biodegradable. Degradable hydrogels canbe synthesized using Atom Transfer Radical Polymerization (ATRP) throughco-polymerization of the HEMA with polymerizable luminescent dyesdescribed herein. Porous sensor scaffolds, based on non-degradable anddegradable glucose-sensing hydrogels, can be generated by using asphere-templating fabrication technique. Degradable and non-degradableHEMA reagents and polymerizable dye will be polymerized over templatingmicrospheres, which are subsequently dissolved away with solvent togenerate desirable non-degradable and degradable scaffolds. Briefly,using controlled ATRP, HEMA will be polymerized in the presence ofbi-functional degradable PCL-based ATRP initiator and cross-linker. Inthis synthesis scheme, pHEMA chains grow at the same rate from bothsides of degradable initiator, resulting in degradation products with amolecular weight (MW) that is half that of the parent polymer. Bycontrolling the MW of the parent polymer and the PEG and PCL units inthe initiator and/or crosslinker, the degradation rate of the polymerscan be varied. Limiting the MW of the parent polymer to 10 kDa resultsin degradation products that can be cleared by the body and an increaseddegradation rate while still preserving the hydrogel's mechanicalstrength.

In certain embodiments, the polymers provided herein arestimuli-responsive, e.g., temperature or pH-sensitive polymers. Onenon-limiting example of such a stimuli-responsive polymer is atemperature-sensitive polymer derived from co-polymerization of NIPAM.Such polymers are useful for implantation of the sensor including saidpolymers in a desired location within tissue by first dissolving thepolymer in a suitable for injection media at a lower than bodytemperature and then injecting the resulting solution into the tissueand/or at desired location of the body. As the polymer is subjected to ahigher (e.g., body) temperature, it precipitates in or near the site ofthe injection where monitoring of the analyte is required.

C. Sensors

In some embodiments, the polymer may be incorporated into a sensoruseful for detection of an analyte. The detection of the analyte can bein vitro or in vivo. The polymer may have the molecules of FormulaeI-IIIH and optionally other polymerizable monomers covalently bound tothe polymer backbone. The molecules of Formulae I-IIIE can be attachedto, e.g. via a covalent bond or other means, or contained withinnanoparticle carriers or microparticle carriers or other carriers thatare attached to or contained within the polymer. Such carriers may becovalently bound to the polymer backbone. In some embodiments, the word“polymer” is used interchangeably with the word “sensor.”

In an embodiment, the sensor may include catalase. As described in U.S.Pat. No. 6,858,403, which is hereby incorporated herein by reference inits entirety, catalase can be used to remove hydrogen peroxide inhydrogel-based sensors.

In one embodiment, the sensor may be a solid material that could be inform of a slab, disc, rod, cylinder, particle or powder. In a specificembodiment, the sensor is in the form of a rod. In another embodiment,the sensor is in the form of a cylinder. In yet other embodiment, thesensor is in the form of a disc.

In another embodiment, the polymer may be, or may be incorporated into,a tissue-integrating scaffold to provide a tissue-integrating sensor (asdescribed in the US patent application 2012/0265034, which isincorporated herein by reference). In an embodiment, thetissue-integrating scaffold may be constructed with materials and/ormicro-architecture such that the scaffold promotes tissue-integrationand/or vascularization. For example, porous scaffolds provide tissuebiomaterial anchoring and promote in-growth throughout the pores. Theresulting “hallway” or “channel” pattern of tissue growth are healthy,space-filling masses that persist over time and promote host cellintegration. Most or all of the pores of the biomaterials describedherein may be interconnected (co-continuous). The co-continuous porestructure of the biomaterials promotes space-filling in-growth of cellsin the implant, which in turn limits the foreign body response and leadsto long-term (greater than one week and up to years) persistence of theimplant's ability to act as a sensor. Alternative structures thatprovide tissue integrating scaffolds include fibers (e.g., 1 to 10 ormore microns in diameter, such as 5, 6, 7, 8, 9, 10 or more microns),which may be arranged in non-random or random configuration.Tissue-integrating scaffolds (in any configuration) can also be formedby multiphoton polymerization techniques. Kaehr et al. (2008) Proc.Nat'l. Acad. Sci. USA 105 (26):8850-8854; Nielson et al. (2009) Small1:120-125; Kasprzak, Doctoral Dissertation, Ga. Institute of Technology,May 2009.

The polymers, which may be in the form of a tissue-integrating scaffold,may include any material in combination with the compound of FormulaeI-IIIH, including but not limited to synthetic polymers,naturally-occurring substances, or mixtures thereof. Exemplary syntheticpolymers include, but are not limited to polyethylene glycol (PEG),2-hydroxyethyl methacrylate (HEMA), silicone rubber,poly([epsilon]-caprolactone) dimethylacrylate, polysulfone, (poly)methymethacrylate (PMMA), soluble Teflon-AF, (poly) ethylenetetrapthalate(PET, Dacron), Nylon, polyvinyl alcohol, polyacrylamide, polyurethane,and mixtures thereof. Exemplary naturally-occurring materials include,but are not limited to, fibrous or globular proteins, complexcarbohydrates, glycosaminoglycans, extracellular matrix, or mixturesthereof. Thus, the polymer scaffold may include collagens of all types,elastin, hyaluronic acid, alginic acid, desmin, versican, matricelluarproteins such as SPARC (osteonectin), osteopontin, thrombospondin 1 and2, fibrin, fibronectin, vitronectin, albumin, chitosan etc. Naturalpolymers may be used as the scaffold or as an additive.

In certain embodiments, the polymer includes a hydrogel. For example,the polymer may include a hydrogel, for example by reacting hydroxyethylmethacrylate (HEMA) and a compound of Formulae I-IIE with one or moreco-monomer to form poly (hydroxyethyl methacrylate), pHEMA-copolymer.Various co-monomers can be used in combination to alter thehydrophilicity, mechanical and swelling properties of the hydrogel (e.g.PEG, NVP, MAA). Non-limiting examples of polymers include 2-hydroxyethylmethacrylate, polyacrylamide, N-vinylpyrrolidone,N,N-dimethylacrylamide, poly(ethylene glycol) monomethacrylate (ofvarying molecular weights), diethylene glycol methacrylate,N-(2-hydroxypropyl)methacrylamide, glycerol monomethacrylate,2,3-dihydroxypropyl methacrylate and combinations thereof. Non-limitingexamples of cross-linkers include tetraethylene glycol dimethacrylate,poly(ethylene glycol) (n) diacrylate (of varying molecular weights),ethoxylated trimethylolpropane triacrylate, bisacrylamide andcombinations thereof. Non-limiting examples of initiators includeirgacure Series (UV), Azobisisobutyronitrile (AIBN) (thermal), AmmoniumPersulfate (APS) (thermal).

The polymer may be a sphere-templated hydrogel, for instance an inversecolloid crystal, for example as described in U.S. Patent Publication No.2008/0075752 to Ratner, et al., which is incorporated herein byreference, or other tissue integrating materials.

The polymer may be degradable, either by the body (biodegradable) or bythe application of an external initiator to start or speed up thedegradation process (e.g. UV, ultrasonics, radio frequency, or otherexogenous sources to initiate degradation.). For example, the polymermay be include any biodegradable or bioresorbable polymers, includingbut not limited to degradable forms of alginates, poly(lactic acid),poly(vinyl alcohol), polyanhydrides, poly(glycolic acid), microporouspolyesters, microporous polyethers and cross-linked collagen. Onespecific example is UV-photopolymerization of poly(ethyleneglycol)-diacrylate and acrylated protease-degradable peptides and VEGFas described by Phelps, et al (2010) Proc. Nat'l. Acad. Sci. USA 107(8):3323-3328.

Other specific examples are polymers described by Kloxin et al (2009)Science 324:59-63 and U.S. Pat. No. 6,013,122 whose degradation iscontrolled through exposure to exogenous energy forms, as well as byAlexeev et al. (2003) Anal. Chem. 75:2316-2323; Badylak et al. (2008)Seminars in Immunology 20:109-116; Bridges et al. (2010) 94 (1):252-258;Isenhath et al. (2007) Research 83A:915-922; Marshall et al. (2004)Polymer Preprints, American Chemical Society, Division of PolymerChemistry 45:100-101; Phelps et al. (2010) Proc Nat'l Acad Sci USA. 107(8):3323-8; Ostendorf and Chichkov (2006) Two Photon Polymerization: ANew Approach to MicroMachining, Photonics Spectra; Ozdemir et al. (2005)Experimental and Clinical Research, Plast. Reconstr. Surg. 115:183; U.S.Patent Publication No. 20080075752; Sanders et al. (2003) Journal ofBiomedical Materials Research Part A 67A(4): 1181-1187; Sanders et al.(2002) Journal of Biomedical Materials Research 62 (2):222-227; Sanderset al. (2003) Journal of Biomedical Materials Research 65 (4):462-467;Sanders et al. (2005) Biomaterials 26:813-818; Sanders et al. (2005)Journal of Biomedical Materials Research Part A 72 (3):335-342; Sanders(2003) Journal of Biomedical Materials Research 67 (4):1412-1416;Sanders et al. (2000) Journal of Biomedical Materials Research 52(1):231-237; and Young Min Ju et al. (2008) J Biomed Mater Res 87A:136-146.

In addition, the polymer may be constructed such that it has conduits,pores or pockets that are hollow or filled with degradable, angiogenic,or other substances (e.g. stem cells). As noted above, once in the body,the biodegradation of the material filling the conduits, pores orpockets, creates space for tissue, including capillaries to integratewith the material. The degradable material that initially fills theconduits, pores, or pockets, may enhance vessel growth or tissue growthwithin the scaffold. This architecture promotes new vessel formation andmaintains healthy viable tissue within and around the implant.

The polymer may be constructed such that it is permeable to analytes ofinterest (e.g., glucose can diffuse into a hydrogel scaffold and reachthe sensing moieties that are embedded within the hydrogel matrix).

The polymer can be of any suitable form, including, but not limited toblock-like (or any thickness), cube-like, disk-shaped, cylindrical,oval, round, random or non-random configurations of fibers and the like.In certain embodiments, the sensor includes one or more fibers, whichmay be organized in a non-random fashion (e.g., grid, layered grid,etc.) or in a random fashion.

The polymer described herein may be combined with (or made up of)sensing moieties that detect one or more analytes. In one embodiment,the sensing moiety is the residue of compound of Formulae I-IIIHincorporated into the hydrogel scaffold.

In another embodiment, the polymer, which may be in the form of atissue-integrating scaffold, includes, in addition to the residue of afirst compound of Formulae I-IIIH, a second sensing moiety. In oneembodiment, the second sensing moiety is a second compound of FormulaeI-IIIH.

In another embodiment, the polymer, e.g., in the form of atissue-integrating scaffold, may be a multi-analyte sensor where glucoseis one of two or more analytes detected and reported. In thisembodiment, the polymer includes a residue of compound of FormulaeI-IIIH for detection of glucose, and a second sensing moiety fordetection of another substance. Non-limiting examples of analytes thatmay be detected by the sensing moieties include oxygen, reactive oxygenspecies, glucose, lactate, pyruvate, cortisol, creatinine, urea, sodium,magnesium, calcium, potassium, vasopressin, hormones (e.g., Luteinizinghormone), pH, cytokines, chemokines, eicosanoids, insulin, leptins,small molecule drugs, ethanol, myoglobin, nucleic acids (RNAs, DNAs),fragments, polypeptides, single amino acids and the like.

In some embodiments, the sensing moieties, e.g., the polymers mayinclude the residue of compound of Formulae I-IIIH that are reversibleluminescent binding molecules. To measure an analyte such as glucose inthe tissue, the polymer is illuminated from a patch reader on top of theskin above the implant with a light of a wavelength that can permeatethe skin, e.g., with 650 nm light, at desired intervals over thelong-term life of the implant (e.g., every 5-60 minutes over a period of90 days or more). The amount of luminescent signal (e.g., from aluminescent molecule) detected is proportional to the concentration ofanalyte (e.g. glucose) in the tissue.

In another embodiment, internal reference control materials can beemployed that facilitate correcting for tissue optical variation. Theimplanted biosensor may reside 1-6 mm, 2-6, mm, 3-6 mm, 3-4 mm, or 3-5mm under the surface of the skin. It is well known that in skinexcitation light and emitted fluorescent light in the near infraredrange are highly scattered as the light traverses the tissue between thereader patch and the implant. The extent of absorption and scattering isaffected by physical properties such as temperature or by tissuecomposition, including but not limited to variations in blood perfusion,hydration, and melanin concentration. Skin variations can occur betweenusers or between different time points for a single patient, and thesevariations can affect the fluorescence excitation and emissions signalscausing in accurate signals for the analyte-specific signal.Accordingly, a separate luminescent molecule with emission spectradistinguishable from the analyte-specific luminescence can beimmobilized into the scaffold. The luminescence from the molecule can bemeasured separately from the analyte-specific luminescence to measure asignal that informs about variations in tissue composition. The seconddye selected for this purpose may have a similar response to tissuevariations as the analyte-specific dye.

In some embodiments, the sensors may be tissue-integrating sensors whichinclude one or more cylindrical shaped elements (e.g., fibers) thateliminate or greatly reduce the foreign body response as compared tocurrently available implants. Moreover, the average diffusion distancesfrom the capillary supply to all parts of the sensing media arecomparable to native tissue, unlike other known sensors.

The overall dimensions of the sensing media (implantable sensor) varyaccording to the subject and/or the analyte(s) to be measured. Theimplant is between about 0.001 mm to about 2 mm in thickness (or anyvalue therebetween) and between about 1 mm and about 1 cm in diameter(or an equivalent cross sectional area of a non-circular shape, forexample length/width) and 15 mm in length or less, for example, adisk-shaped sensor that is 2 mm or less thick and 10 mm or less indiameter. In certain embodiments, the approximate sensor size isapproximately 100-1000 microns in diameter and has the length of between0.25 mm and 10 mm. The size of the tissue-integrating sensing media indisk form may be 2 mm or less thick and 10 mm or less in diameter.

Another aspect is a tissue-integrating biosensor system forsemi-continuous, continuous, and/or long-term use within a mammalianbody.

One advantageous property of the polymers and sensors described hereinis their stability. In one aspect, the sensor is stable in a mammaliantissue for a long period of time, e.g., longer than a week, longer thana month, longer than 2 months, longer than 6 months.

EXAMPLES

NMR spectroscopic data were recorded on a 400 MHz instrument at roomtemperature. NMR spectra were calibrated to the solvent signals ofdeuterated DMSO-d₆, MeOH-d₄ or CDCl₃. The following abbreviations areused to indicate the signal multiplicity: s (singlet), d (doublet), t(triplet), q (quartet), quin (quintet), br (broad), m (multiplet).Analytical HPLC-MS data were recorded on a HPLC system with a C18reversed-phase silica gel column coupled to an electrospray ionization(ESI) mass-spectrometer. Listed UV/Vis absorbance maxima were recordedby HPLC DAD in the eluent system (acetonitrile/water+0.1% HCOOH).Commercially available monomers and chemical building blocks werepurchased from Polysciences, Sigma-Aldrich, VWR, Combi-Blocks, AcrosOrganics, Oakwood Chemical, AK Scientific, and Strem Chemicals. Some ofthe advanced intermediates were synthesized by BioDuro.

Synthesis of Exemplary Compounds of Formulae I-IIIH Synthesis ofCompound 1

General Procedure I. Preparation ofN-[2-bromo-3-(phenylamino)-2-propenylidene]-benzenammonium bromide 1-1

A solution of aniline (17.7 mL, 194 mmol) in anhydrous EtOH (25 mL) wasadded dropwise to a pre-cooled (0° C.) solution of mucobromic acid (25g, 97 mmol) in anhydrous EtOH (75 mL). The reaction mixture was stirredfor 1 h and then was concentrated in vacuo to 50 mL. The productcrystallized from the concentrated solution upon storage at 4° C. for 3days. The crystals were collected by filtration and rinsed with acetoneand cold EtOH to yield the title compound 1-1 as an orange/yellow solid(24.2 g, 83%).

General Procedure II. Preparation of Pentamethine Cyanine Fluorophore(Cy5). Preparation of2-[3-bromo-5-(1,3-dihydro-1,3,3-trimethyl-2H-indol-2-ylidene)-1,3-pentadien-1-yl]-1,3,3-trimethyl-3H-indoliumiodide 1-2

A solution of compound 1-1 (1.01 g, 2.65 mmol),1,2,3,3-tetramethyl-3H-indolium iodide (4.0 g, 13.3 mmol), and sodiumacetate (2.16 g, 26.5 mmol) in acetic anhydride (40 mL) was heated at80° C. for 20 min. The reaction was then diluted with DCM and washedwith water and brine. The DCM layer was then dried over MgSO₄ andconcentrated in vacuo. The residue was purified by flash chromatography(SiO₂, eluted with DCM and MeOH) to afford the title product 1-2 (758mg, 48%).

General Procedure III. Suzuki-Miyaura Cross-Coupling with PinacolBorate. Preparation of2-[3-(4-aminomethylphenyl)-5-(1,3-dihydro-1,3,3-trimethyl-2H-indol-2-ylidene)-1,3-pentadien-1-yl]-1,3,3-trimethyl-3H-indoliumiodide 1-3

In a flame-dried flask, intermediate 1-2 (758 mg, 1.28 mmol),4-aminomethylphenylboronic acid pinacol ester hydrochloride (600 mg,2.57 mmol), and cesium carbonate (1.25 g, 3.85 mmol) were mixed withEtOH (50 mL) and water (25 mL). The mixture was degassed by bubbling dryargon at 60° C. for 1 h. Palladium(II) acetate (60 mg, 0.128 mmol) andtriphenylphosphine (200 mg, 0.514 mmol) were then added and the reactionmixture was stirred for 16 h at 60° C. under argon. Additional4-aminomethylphenylboronic acid pinacol ester hydrochloride (90 mg,0.386 mmol), Palladium(II) acetate (60 mg, 0.128 mmol), andtriphenylphosphine (200 mg, 0.514 mmol) were then added and reaction wasstirred for 16 h at 60° C. under Ar. The reaction mixture was thenconcentrated in vacuo, diluted with DCM and filtered through Celite®.The filtrate was washed with water and brine, then dried over MgSO₄, andconcentrated in vacuo. The residue was purified by flash chromatography(SiO₂, eluted with 0.09% HCl in MeOH and DCM). The pure product wasdissolved in DCM and washed with saturated NaHCO₃ 3 times. The DCMportion was then dried over MgSO₄ and concentrated in vacuo to yieldproduct 1-3 (258 mg, 41%).

Preparation of N-{3-[(4-formylphenyl)methylamino]propyl}methacrylamide1-4

A mixture of N-(3-aminopropyl)methacrylamide hydrochloride (APMA.HCl;4.47 g, 25.1 mmol) and K₂CO₃ (13.8 g, 100.5 mmol) in anhydrous MeOH (10mL) was stirred for 15 min and then diluted with anhydrous DCM (100 mL).4-Bromomethyl-benzaldehyde (2 g, 10.0 mmol) and triethylamine (5 mL,35.8 mmol) were added and the reaction mixture was stirred for 16 h.Then the mixture was filtered, a small amount of 4-methoxyphenol (MEHQ,polymerization inhibitor) was added to the filtrate, and it wasconcentrated in vacuo. Drying under high vacuum afforded the titlecompound 1-4 as a white solid (3.25 g, 124%).

General Procedure IV. Reductive Amination. Preparation of Compound 1-6

A solution of amine 1-3 (258 mg, 0.419 mmol), glacial acetic acid (0.15mL, 2.50 mmol), and aldehyde 1-4 (319 mg, 1.20 mmol) in anhydrous MeOH(15 mL) and anhydrous DCE (5 mL) was stirred for 15 minutes overmolecular sieves (3 Å, 200 mg). Then sodium triacetoxyborohydride (400mg, 1.88 mmol) was added in three portions with 10 min intervals. Uponcompletion of the reaction, the slurry was filtered and the filtrateconcentrated in vacuo to approximately 5 mL. The concentrate was dilutedwith DCM, washed with saturated NaHCO₃ and brine, dried over MgSO₄, andconcentrated in vacuo. The residue was purified by flash chromatography(SiO₂, eluted with DCM and 0.05% HCl in MeOH). The purified product wasdissolved in DCM, washed with sat. NaHCO₃ 3 times, dried over MgSO₄, andconcentrated in vacuo to yield the title product 1-6 (198 mg, 55%).

General Procedure V. Alkylation with Unprotected2-Bromomethylphenylboronic Acid. Preparation of Compound 1

To a solution of diamine 1-6 (198 mg, 0.23 mmol) in anhydrous DCM (15mL) and anhydrous DMF (2 mL), K₂CO₃ (257 mg, 1.86 mmol),2-bromomethylphenylboronic acid (300 mg, 1.4 mmol), and DIPEA (0.4 mL,2.3 mmol) were added. The reaction mixture was stirred for 1 h andaddition of 2-bromomethylphenylboronic acid (150 mg, 0.697 mmol) andDIPEA (0.081 mL, 0.465 mmol) was repeated. After 1 h, fresh portion of2-bromomethylphenylboronic acid (450 mg, 2.8 mmol) was added and themixture was stirred for 16 h. The crude product was precipitated byhexane, collected by centrifugation, and purified by flashchromatography (SiO₂, eluted with DCM and 0.05% HCl in MeOH. The pureproduct was dissolved in DCM, washed with saturated NaHCO₃ 3 times,dried over MgSO₄, and concentrated in vacuo to yield the title productcompound 1 (78 mg, 30% yield). HPLC-MS: m/z 1000.7 (calcd. 1000.6 forM⁺); λ_(max)=650 nm.

Preparation of Compound 2

General Procedure VI. Alkylation of 2,3,3-trimethyl-3H-indole withSultone. Preparation of Compound 2-1

A mixture of 2,3,3-trimethyl-3H-indole (9.90 g, 62.3 mmol) and1,3-propanesultone (11.4 g, 93.4 mmol) in anhydrous MeCN (150 mL) washeated at 90° C. in a sealed vessel overnight. Then the mixture waspoured into diethyl ether (500 mL) under vigorous stirring and thenfiltered. The solid product was dried under high vacuum to afford theintermediate 2-1 as a pink solid (15 g, 86% yield).

Compound 2 was prepared from intermediate 2-1, following generalprocedures II, III, IV, and V, as outlined in the scheme above. HPLC-MS:m/z=1217.1 (calcd. 1216.5 for M⁺); λ_(max)=650 nm.

Preparation of Compound 3

Preparation of Compound 3-1

To a stirred solution of 2,4-dimethylpyrrole (5.7 g, 60 mmol) in DCM(120 mL) p-(chloromethyl)benzoyl chloride (5.67 g, 30 mmo) was addeddropwise at room temperature and under nitrogen atmosphere. The mixturewas stirred for 12 h. Triethylamine (20 mL) was added, the reactionmixture was stirred for additional 1 h at room temperature, followed byaddition of boron trifluoride diethyl etherate (20 mL). The reactionmixture was stirred for 2 h, and concentrated under reduced pressure.The residue was purified by column chromatography (SiO₂, eluted withhexanes/EtOAc=8:1) to give intermediate 3-1 (3.0 g, 27% yield) as orangesolid.

Preparation of Compound 3-2

To a mixture of compound 3-1 (3.75 g, 10.0 mmol) in DMF (60 mL) wasadded sodium azide (0.98 g, 15.0 mmol) at room temperature. Theresulting mixture was stirred at 40° C. overnight, then diluted withwater (500 mL), and extracted with EtOAc (3×200 mL). The organic layerswere combined, washed with brine (3×100 mL), dried over sodium sulfate,filtered, and concentrated to give compound 3-2 (2.6 g, 75% yield) asbrown solid, which was used directly for the next step without furtherpurification.

Preparation of Compound 3-3

To a solution of compound 3-2 (2.05 g, 5.78 mmol, 1.0 eq) in THF (100mL) was added triphenylphosphine (2.07 g, 7.09 mmol) and water (10 mL)at room temperature. The resulting mixture was stirred at 50° C.overnight under nitrogen atmosphere. Then the mixture was concentratedunder reduced pressure. The residue was purified by flash chromatography(SiO₂, eluted with DCM/EtOAc=1:1, then DCM/MeOH=10:1 to afford compound3-4 (1.5 g, 81% yield) as brown solid.

Compound 3 was prepared from intermediate 3-3 following generalprocedures IV and V. HPLC-MS: m/z 867.2 (calcd. 866.5 for M+H⁺);λ_(max)=502 nm.

Preparation of Compound 4

General Procedure VII. Preparation of BODIPY Fluorophore from Aldehydeand Pyrrole. Preparation of Compound 4-1

A mixture of 4-nitrobenzaldehyde (1.20 g, 7.9 mmol), 2,4-dimethylpyrrole(1.6 mL, 15.9 mmol), and TFA (0.12 mL, 1.6 mmol) in anhydrous DCM (300mL) was stirred at room temperature for 3 h. Then2,3-dichloro-5,6-dicyano-1,4-benzoquinone (1.80 g, 7.9 mmol) was addedand the darkened reaction mixture was stirred for 1 h. Triethylamine (11mL, 79 mmol) and boron trifluoride diethyl etherate (12.7 mL, 103 mmol)were subsequently added and the mixture was stirred for 1 h. Thereaction mixture was then washed with water (2×500 mL) and brine (250mL). Organic layer was dried over anhydrous Na₂SO₄, filtered, andconcentrated in vacuo. The residue was purified by flash chromatography(SiO₂, eluted with gradient of 0% to 30% EtOAc in hexanes). Yield: 0.60g (21%).

Preparation of Compound 4-2

A mixture of intermediate 4-1 (1.23 g, 3.3 mmol), and iron powder (3.53g, 63.3 mmol) in THF (75 mL), 0.5 M methanolic HCl (20 mL), and water (5mL) was refluxed for 2 h. Then the reaction mixture was concentrated invacuo, the residue was redissolved in DCM (100 mL), filtered, andconcentrated again. The residue was purified by flash chromatography(SiO₂, eluted with gradient of 0% to 30% EtOAc in hexanes) yielding thetitle compound 4-2 (0.85 g, 76% yield) as a red-orange solid.

Compound 4 was prepared from intermediates 4-2 and 1-4 following generalprocedures IV and V. HPLC-MS: m/z 852.5 (calcd. 852.4 for M+H⁺);λ_(max)=500 nm. ¹H NMR (400 MHz, MeOH-d₄+NaOD) δ ppm 7.61 (d, J=7.6 Hz,2H), 7.23-7.33 (m, 4H), 6.96-7.13 (m, 4H), 6.91-6.96 (m, 2H), 6.88 (d,J=8.7 Hz, 2H), 6.78 (d, J 8.7 Hz, 2H), 6.00 (s, 2H), 5.49 (s, 1H), 5.25(q, J=1.1 Hz, 1H), 5.09 (br. s., 2H), 4.70 (br. s., 2H), 3.83 (br. s.,2H), 3.58 (br. s., 2H), 3.06 (t, J=6.5 Hz, 2H), 2.41 (t, J=7.0 Hz, 2H),1.82 (q, J=1.1 Hz, 3H), 1.73 (quin, J=6.7 Hz, 2H), 1.50 (s, 6H). Sixmethyl protons from BODIPY overlapped with the solvent peak.

Preparation of Compound 6

General Procedure VIII. Nucleophilic Substitution at Cy7 Fluorophore.Preparation of2-(2-{2-chloro-3-[(1,3-dihydro-3,3-dimethyl-1-propyl-2H-indol-2-ylidene)ethylidene]-2-(4-tert-butylcarbamateaminomethylphenoxy)-1-cyclohexen-1-yl}ethenyl)-3,3-dimethyl-1-propylindoliumiodide 6-2

A mixture of tert-butyl (4-hydroxyphenylmethyl)carbamate (348 mg, 1.5mmol), IR-780 (6-1) (500 mg, 0.75 mmol), and cesium carbonate (487 mg,1.5 mmol) in anhydrous DCM (50 mL) was stirred at 40° C. under argon.After 1 h, the reaction mixture was filtered through Celite® and thefiltrate was concentrated in vacuo. The crude residue was purified byflash chromatography (SiO₂, eluted with DCM and MeOH) to yield the titleproduct 6-2 (1.3 g, quant.).

General Procedure IX. Boc Deprotection. Preparation of2-(2-{2-chloro-3-[(1,3-dihydro-3,3-dimethyl-1-propyl-2H-indol-2-ylidene)ethylidene]-2-(4-aminomethylphenoxy)-1-cyclohexen-1-yl}ethenyl)-3,3-dimethyl-1-propylindoliumiodide 6-3

Intermediate 6-2 (625 mg, 0.73 mmol) was dissolved in neat TFA (10 mL)at 0° C. The reaction mixture was allowed to warm up to room temperatureover 5 min while stirring under argon. Then the solution wasconcentrated in vacuo. The crude product was purified by flashchromatography (SiO₂, eluted with DCM and MeOH) to afford the pureproduct 6-3 (466 mg, 88%).

Preparation of Compound 6-4

To a solution of intermediate 6-3 (895 mg, 1.19 mmol) in anhydrous MeOH(40 mL) over molecular sieves (3 Å, 500 mg), glacial acetic acid (0.35mL, 6.0 mmol) and intermediate 1-4 (752 mg, 1.49 mmol) were added. Thereaction mixture was stirred for 15 min at room temperature, followed byportion-wise addition of sodium triacetoxyborohydride (3×277 mg, 3.90mmol) with 10 min intervals. 15 min after the last addition, thereaction mixture was filtered and the filtrate was concentrated invacuo. The residue was then diluted with DCM and washed with saturatedNaHCO₃ and brine. The DCM layer was then dried over MgSO₄ andconcentrated in vacuo. The crude product was purified by flashchromatography (SiO₂, eluted with DCM and MeOH) yielding the titlecompound 6-4 (415 mg, 35%).

Preparation of Compound 6

To a solution of intermediate 6-4 (400 mg, 0.40 mmol) in anhydrous DMF(4 mL) 2-bromomethylphenylboronic acid (600 mg, 2.8 mmol) and K₂CO₃(1.35 g, 10.0 mmol) were added in three portions. The reaction mixturewas stirred for 16 h at room temperature and then concentrated in vacuo.The residue was purified by flash chromatography (SiO₂, eluted with0.05% HCl in MeOH and DCM). The pure product was taken up into DCM andwashed with saturated NaHCO₃ three times. The DCM portion was then driedover MgSO₄ and concentrated in vacuo to yield the title compound 6 (90mg, 18%). HPLC-MS: m/z 1138.5 (calcd. 1138.7 for M⁺); λ_(max)=775 nm. ¹HNMR (400 MHz, MeOH-d₄) δ ppm 7.96 (d, J=14.3 Hz, 1H), 7.63 (d, J=7.3 Hz,1H), 7.36-7.44 (m, 6H), 7.32 (m, J=7.6, 7.6 Hz, 3H), 7.23-7.29 (m, 3H),7.15-7.22 (m, 7H), 7.12 (m, J=7.3, 7.3 Hz, 4H), 6.14 (d, J=14.2 Hz, 2H),5.52 (s, 1H), 5.22 (s, 1H), 4.13 (br. s., 2H), 4.04 (t, J=7.4 Hz, 4H),4.03 (s, 2H), 3.65 (br. s., 2H), 3.52 (s, 2H), 3.50 (br. s, 2H), 3.35(s, 1H), 3.10 (t, J=6.0 Hz, 2H), 2.74 (t, J=6.0 Hz, 4H), 2.54-2.68 (m,2H), 2.04 (quin, J=6.0 Hz, 2H), 1.86-1.96 (m, 2H), 1.80 (m, J=7.7, 7.7,7.7 Hz, 4H), 1.76 (s, 3H), 1.25 (s, 12H), 0.99 (t, J=7.4 Hz, 6H).

Preparation of Compound 5

Preparation of2-[2-(3-{2-[1,3-dihydro-3,3-dimethyl-1-(4-sulfobutyl)-2H-indol-2ylidene]ethylidene}-2-(4-aminomethylphenoxy)-1-cyclohexen-1-yl)ethenyl]-3,3-dimethyl-1-(4-sulfobutyl)-3H-indolium,monosodium salt (5-2)

A mixture of IR-783 (5-1) (4 g, 5.54 mmol), tert-butyl(4-hydroxyphenyl-methyl)carbamate (2.47 g, 11.1 mmol), and cesiumcarbonate (3.6 g, 11.1 mmol) in anhydrous DCM (100 mL) was stirred for16 h at room temperature. The reaction mixture was filtered throughCelite and the filtrate was concentrated in vacuo. The crudeintermediate was dissolved in TFA (25 mL), the solution was stirred for5 min and then concentrated in vacuo. The residue was purified byreversed-phase flash chromatography (C18 SiO₂, eluted with gradient of0.09% HCl in MeOH). The pure product was isolated by basification ofcombined and concentrated fractions with saturated NaHCO₃, followed bytriple extraction with DCM. The combined DCM layers were then dried overMgSO₄ and concentrated in vacuo to yield the title product 10-2 (5.4 g,quant.). HPLC-MS: m/z 1326.0 (calcd. 1326.6); λ_(max)=775 nm.

Preparation of Compound 7

By analogy with compound 6, compound 7 was prepared from IR-780 and4-N-Boc-aminophenol following general procedures VIII, IX, IV, and V.HPLC-MS: m/z 1124.5 (calcd. 1124.7); λ_(max)=775 nm. ¹H NMR (400 MHz,MeOH-d₄) δ ppm 7.97 (d, J 14.2 Hz, 2H), 7.60 (br. s., 1H), 7.34-7.42 (m,5H), 7.20-7.33 (m, 11H), 7.13-7.20 (m, 3H), 6.92 (s, 4H), 6.11 (d,J=14.2 Hz, 2H), 5.59 (s, 1H), 5.33 (s, 1H), 4.58 (s, 2H), 4.44 (s, 2H),4.16 (br. s., 2H), 4.05 (t, J=7.4 Hz, 4H), 4.00 (br. s, 2H), 3.08 (t,J=6.2 Hz, 2H), 2.69 (t, J=6.0 Hz, 4H), 2.75 (br. s, 2H), 2.00 (m, J=6.4Hz, 2H), 1.72-1.89 (m, 9H), 1.30 (s, 12H), 1.01 (t, J=7.4 Hz, 6H).

Preparation of Compound 10

Preparation of10-[(3-methacrylamidoprop-1-yl)aminomethyl]-9-anthracenecarboxaldehyde10-2

To a solution of N-(3-aminopropyl)methacrylamide hydrochloride (1.00 g,5.78 mmol) in anhydrous MeOH (5 mL), a solution ofanthracene-9,10-dicarboxaldehyde (2.7 g, 11.56 mmol) in anhydrous DCM(10 mL) was added. The resulting mixture was diluted with anhydrous THF(150 mL) and acetic acid (0.52 mL, 8.6 mmol), followed by addition ofsodium triacetoxyborohydride (2.45 g, 11.56 mmol). The mixture wasstirred at room temperature. After 1 h, a second portion of sodiumtriacetoxyborohydride (1.2 g, 5.75 mmol) was added and the reaction wasstirred at room temperature for 2 h. The reaction mixture was thendiluted with DCM and washed with sat NaHCO₃ and brine. The DCM portionwas then dried over MgSO₄ and concentrated in vacuo. The crude productwas purified by flash chromatography (SiO₂, eluted with MeOH and DCM) toafford the title compound 10-2 (424 mg, 20%).

Preparation of Compound 10-3

A mixture of intermediate 5-2 (294 mg, 0.351), molecular sieves (3 Å),glacial acetic acid (200 μL, 1.4 mmol), and intermediate 10-2 (190 mg,0.528 mmol) in anhydrous MeOH (10 mL) and DCE (5 mL) was stirred at roomtemperature for 15 minutes. Then sodium triacetoxyborohydride (112 mg,0.528 mmol) was added and then the addition was repeated three moretimes over 20 h. The reaction was then concentrated in vacuo toapproximately 2 mL, and basified by saturated NaHCO₃. The crude productwas purified by reversed-phase flash chromatography three times (C18SiO₂, eluted with gradient of water and MeOH with 0.1% TFA) to affordpure title product 10-3 (105 mg, 21.7%).

Preparation of Compound 10

A solution of intermediate 10-3 (90 mg, 0.065 mmol) and DIPEA (42.2 mg,0.327 mmol) in anhydrous DCM (8 mL) was stirred for 10 min, followed bythe addition of 2-bromomethylphenyl boronic acid (58.5 mg, 0.327 mmol).After 90 min, the reaction mixture was diluted with hexanes andcentrifuged. The precipitate purified by reversed-phase flashchromatography (C18 SiO₂, eluted with gradient of water and MeOH). Puretitle compound 10 was obtained by precipitating from concentrated DCMsolution with diethyl ether (61 mg, 64%). HPLC-MS: m/z 1428.6 (calcd.1426.7 for M+H⁺); λ_(max)=760 nm. ¹H NMR (400 MHz, MeOH-d₄) δ ppm 8.42(d, J=8.2 Hz, 2H), 8.31 (d, J=8.8 Hz, 2H), 7.94 (d, J=14.2 Hz, 2H),7.34-7.59 (m, 9H), 7.16-7.34 (m, 9H), 7.12 (d, J=8.5 Hz, 2H), 6.94-7.06(m, 4H), 6.15 (d, J=14.2 Hz, 2H), 5.37 (s, 1H), 5.18 (quin, J=1.3 Hz,1H), 4.41 (br. s., 2H), 4.13 (br. s., 2H), 4.06 (t, J=6.5 Hz, 4H), 3.60(br. s., 2H), 3.53 (s, 2H), 2.99 (t, J=6.5 Hz, 2H), 2.86 (t, J=6.8 Hz,4H), 2.66-2.80 (m, 6H), 2.04 (quin, J=6.5 Hz, 2H), 1.81-1.97 (m, 10H),1.70 (s, 3H), 1.16 (s, 12H). One benzylic CH₂ group overlapped with thesolvent signal.

Preparation of Compound 8

Preparation of Compound 8-1

By analogy with intermediate 10-3, anthacenecarboxaldehyde 10-2 (272 mg,0.76 mmol) was coupled with Cy5-benzylamine 2-3 (500 mg, 0.69 mmol)under treatment of triacetoxyborohydride (726 mg, 3.4 mmol) and aceticacid (124 mg, 2.1 mmol). The desired product was isolated as a bluesolid (13 mg, 2% yield) after purification by reversed phase flashchromatography (MeOH−water+0.25% HCl).

Preparation of Compound 8

By analogy with synthetic procedure for Compound 10, diamine 8-2 (13 mg,0.012 mmol) was alkylated with 2-bromomethylphenylboronic acid (6.5 mg,0.030 mmol) affording target product (7 mg, 44% yield) as a dark bluesolid. HPLC-MS: m/z 1317.5 (calcd. 1316.6 for M+H⁺); λ_(max)=640 nm.

Preparation of Compound 9

Intermediate 9-1 was prepared from 1,1,2-trimethyl-1H-benzo[e]indolefollowing general procedures VI, II, and III (see intermediate 2-3).Compound 9 was then synthesized from intermediates 10-2 and 9-1following analogous route as described for Compound 8, following generalprocedures IV and V. HPLC-MS: 1417.5 m/z (calcd. 1416.6 for M+H⁺);λ_(max)=630, 685 nm.

Preparation of Compound 11

Preparation of Compound 11-1

Formaldehyde (63.52 g, 0.807 mol, as 38% in water), acetic acid (1500mL), and 3-bromo-N,N-dimethylaniline (323 g, 1.615 mol) were combinedand stirred at 60° C. under argon for 2 h. The reaction mixture was thenconcentrated under reduced pressure. The residue was dissolved in DCM(100 mL), washed with saturated NaHCO₃ and brine, dried over anhydrousNa₂SO₄, filtered, and concentrated under reduced pressure. The residuewas purified by flash chromatography (SiO₂, eluent: DCM/hexanes 1:5).This afforded title intermediate 11-1 (216 g, 65% yield) as a pinksolid.

Preparation of Compound 11-2

To a solution of intermediate 11-1 (30 g, 73 mmol) in anhydrous THF (200mL) cooled to −78° C. under argon atmosphere, sec-butyllithium (1.3 M incyclohexane, 168 mL, 218 mmol) was added dropwise over 30 minutes. Theresulting mixture was stirred at 78° C. for 2 h, followed by addition ofdichlorodimethyl silane (16.9 g, 131.1 mmol). The mixture was allowed towarm up to room temp over 2 h. The reaction was then quenched with 1 MHCl, pH was adjusted to 8 with NaOH, and the mixture was extracted withDCM (3×300 mL). Combined organic layers were washed with brine, driedover anhydrous Na₂SO₄, filtered, and concentrated under reduced pressureto give crude compound 11-2 (28 g) as a green solid. The crude productwas used directly for the next step, without further purification.

Preparation of Compound 11-3

The crude compound 11-2 (28 g, theor. 73 mmol) was dissolved in acetone(300 mL) and cooled to −15° C. To this solution KMnO₄ (42.5 g, 271 mmol)was added portionwise over 30 minutes and the reaction mixture wasstirred for 2 h at −15° C. Reaction then was allowed to warm up to roomtemperature, filtered through Celite®, and the filter cake was rinsedwith acetone. The filtrate was concentrated under reduced pressure. Theresidue was purified by flash chromatography (SiO₂, eluent: DCM). Thisresulted in compound 11-3 (8 g, 26% yield) as a yellow-green solid.

Preparation of Compound 11-4

A mixture of 4-bromobenzylamine (1.0 g, 5.4 mmol), triethylamine (1.50mL, 10.7 mmol) in anhydrous DCM (50 mL) was cooled to 0° C. under argonatmosphere. A solution of 1,2-bis(chlorodimetylsilyl)ethane (1.16 g, 5.4mmol) in anhydrous DCM (20 mL) was added via cannula. The mixture wasstirred for 1 h at 0° C. and then 1 h at room temperature. The solventwas removed in vacuo, the residue was suspended in hexanes and filtered.Filtrate was concentrated in vacuo and used in the next step withoutfurther purification.

General Procedure X. Preparation of Silicon Rosamine Fluorophore ViaLithium-Halogen Exchange with Sec-BuLi. Preparation of Compound 11-5

To a solution of arylbromide 11-4 (theor. 5.4 mmol) in anhydrous THF (20mL) cooled to −78° C. under argon atmosphere, sec-butyllithium (c=1.4 Min cyclohexane, 5.76 mL, 8.1 mmol) was added dropwise. The mixture wasstirred at −78° C. for 1 h. Then a solution of silaxanthone 11-3 (0.17g, 0.5 mmol) in anhydrous THF (10 mL) was added via cannula, and themixture was allowed to warm up to room temperature overnight. Thereaction was quenched with 1 M HCl (10 mL) and stirred for 30 min to 3 h(monitored the progress by LCMS). The pH was adjusted to 8 with NaOH andthe mixture was extracted with DCM. Combined organic layers were driedover anhydrous MgSO₄, filtered, and concentrated in vacuo. The residuewas purified by reversed phase flash chromatography (C18 SiO₂, gradientelution with 0.25% HCl (aq) in MeOH). Yield: 250 mg (quant.) as adark-blue solid.

Compound 11 was synthesized from intermediates 11-5 and 10-2, followinggeneral procedures IV and V. HPLC-MS: m/z 1027.1 (calcd. 1026.5 for M⁺);λ_(max)=650 nm.

Preparation of Compound 12

Compound 12 was synthesized form intermediates 3-3 and 10-2, followinggeneral procedures IV and V. HPLC-MS: m/z 967.4 (calcd. 966.5 for M+H⁺);λ_(max)=500 nm.

Preparation of Compound 13

Preparation of Compound 13-1

A mixture of amine 10-2 (0.61 g, 1.69 mmol), triehylamine (0.55 mL, 3.9mmol), and di-tert-butyl dicarbonate (0.70 g, 3.2 mmol) in THF (20 mL)was stirred at room temperature overnight. The solvent was removed invacuo and the residue was purified by flash chromatography (SiO₂, elutedwith 0 to 10% gradient of MeOH in DCM). Yield: 209 mg (27%) as yellowfoam.

Compound 13 was synthesized from intermediates 7-2, and 13-1 followinggeneral procedures IV, IX, and V. HPLC-MS: m/z 1225.3 (calcd. 1224.7);λ_(max)=780 nm.

Preparation of Compound 14

Preparation of 6-Hydrazinyl-2-Naphthalenesulfonic Acid Hydrochloride14-1

To a cold (0° C.) solution of 6-amino-2-naphthalenesulfonic acidmonohydrate (15.2 g, 68.1 mmol) in aqueous HCl (12 M, 100 mL) a solutionof NaNO₂ in water (25 mL) was added dropwise over 10 min and thereaction mixture was stirred for 45 min at 0° C. Then a solution ofSnCl₂ in HCl (12 M, 25 mL) was added dropwise over 1 h keeping thetemperature at 0° C. The reaction mixture was stirred for 45 min at 0°C. and then for 1.5 h at room temperature. The mixture was concentratedin vacuo and the resulting solid was triturated with acetone. Theprecipitate was rinsed with acetone to yield the title compound 14-1 asa light pink solid (17 g, 90%).

Preparation of Potassium 1,1,2-trimethyl-1H-Benz[e]indole-7-sulfonate14-2

A solution of the intermediate 14-1 (12 g, 68.1 mmol), KOAc (6.39 g,65.1 mmol), and isopropylmethyl ketone (8.41 g, 10.5 mmol) in AcOH (200mL) was heated at 90° C. for 16 h and then was allowed to cool to roomtemperature. The reaction mixture was then concentrated to dryness invacuo, the residue was suspended in acetone, and filtered. The insolublesolid material was washed with EtOH. Combined filtrates wereconcentrated in vacuo. The residue was purified by reversed-phase flashchromatography (C18 SiO₂, eluted with gradient of acetonitrile in water)yielding the title compound 14-2 (7.5 g, 34%).

Preparation of Potassium1,1,2-trimethyl-3-(3-sulfopropyl)-1H-Benz[e]indolium-7-sulfonate 14-3

To a solution of the intermediate 14-2 (5.7 g, 17.4 mmol) in anhydrousDMF (120 mL) 1,3-propanesultone (4.47 mL, 50.9 mmol) was added and thereaction mixture was stirred for 5 h at 100° C. and then wasconcentration in vacuo. The crude product was purified by reversed-phaseflash chromatography (C18 SiO₂, eluted with water) yielding the titlecompound 14-3 as an orange foam (3.1 g, 40%).

Preparation of 2-acetyl-9,10-dimethylanthracene 14-X

To a solution of 9,10-dimethyl anthracene (10.0 g, 48.5 mmol) in carbondisulfide (300 mL), acetyl chloride (4.9 mL, 75.6 mmol) was addedfollowed by aluminum trichloride (9.3 g, 69.8 mmol). The reddish-brownreaction mixture was stirred at room temperature overnight and then at45° C. for 4 h. The reaction was quenched by addition of ice (50 g),conc. HCl (1 mL), and was stirred for 30 min. Then DCM (200 mL) wasadded until all black solid dissolved. The layers were separated, andthe aqueous layer was additionally extracted with DCM. Combined organiclayers were washed with water and dried over MgSO₄, filtered,concentrated in vacuo. The crude product was purified by flashchromatography (SiO₂, eluted with DCM). Obtained 6.7 g of the titleproduct as a yellow solid (56%).

Preparation of 9,10-dimethyl-2-anthracenecarboxylic Acid, 14-4

A solution of 9,10-dimethyl-2-acetylanthracene (7.6 g, 30.6 mmol) indioxane (150 mL) was heated at 80° C., added to a solution of NaOCl(14.5%, 80 mL) and NaOH (6.7%, 50 mL), and stirred for 16 h at 80° C.Then the reaction mixture was diluted with water (100 mL) and acidifiedwith HCl (1 M) until pH 1. The suspension was filtered, and the solidproduct was extensively washed with water to afford compound 14-4 as ayellow solid (6.3 g, 84%).

Preparation of 9,10-dimethyl-2-anthracenecarboxylic Acid Methyl Ester,14-5

A solution of compound 14-4 (6.3 g, 25.1 mmol) and p-toluenesulfonicacid (8.7 g, 50.3 mmol) in MeOH (100 mL) was refluxed for 22 h. Thereaction was then concentrated in vacuo, diluted with DCM, and washedwith saturated NaHCO₃, 1 M NaHCO₃, and brine. The organic layer wasdried over anhydrous MgSO₄, filtered, and concentrated in vacuo to yieldcompound 14-5 as a yellow solid (6.13 g, 92%).

Preparation of 9,10-dimethyl-2-hydroxymethylanthracene, 14-6

A suspension of LiAlH₄ (2.63 g, 69.4 mmol) in anhydrous THF (100 mL) wascooled to 0° C. A solution of compound 14-5 (6.12 g, 23.1 mmol) inanhydrous THF (100 mL) was added dropwise over 15 min. After stirring at0° C. for 45 min, the reaction was quenched by water (12 mL) and NaOH(15%, 3 mL) at 0° C. The reaction mixture was then diluted with diethylether (150 mL) and filtered. The solid was washed with ethyl acetate.Combined filtrate and washing were concentrated in vacuo, then theresidue was dissolved in ethyl acetate and washed with brine. Theorganic layer was dried over anhydrous MgSO₄, filtered, and concentratedin vacuo to yield compound 14-6 as a yellow solid (4.6 g, 86%).

Preparation of 9,10-dimethyl-2-anthracenecarboxaldehyde, 14-7

In a flame dried 500 mL 3-neck flask potassium chlorochromate (5.48 g,25.4 mmol) was suspended in anhydrous 1,2-dichloroethane (100 mL) underargon. Solution of compound 14-6 (4.62 mg, 19.5 mmol) in anhydrous1,2-dichloroethane (150 mL) was added dropwise to the slurry over 20min. After stirring at room temperature for 6 h, the reaction mixturewas filtered through Celite and the plug was rinsed with DCM. Thefiltrate was concentrated in vacuo to yield compound 14-7 as a yellowsolid (720 mg, 15%).

Preparation of 9,10-bis(bromomethyl)-2-anthracenecarboxaldehyde, 14-8

A mixture of compound 14-7 (720 mg, 3.1 mmol) and N-bromosuccinimide(1.20 g, 6.7 mmol) in anhydrous CCl₄ (50 mL) was refluxed for 1 h. Thereaction mixture was then diluted with toluene (100 mL) and cooled to−20° C. for 3 days. The resulting yellow crystals were isolated byfiltration and washed with MeOH to yield compound 14-8 as a yellow solid(830 mg, 69%).

Preparation of Compound 14-9

A mixture of N-(3-aminopropyl)methacrylamide hydrochloride (1.54 g, 8.6mmol), triethylamine (1.25 mL, 8.67 mmol), and compound 14-8 inanhydrous DCM (75 mL) was refluxed for 16 h under argon. Then thereaction mixture was concentrated in vacuo and the residue was purifiedby flash chromatography (SiO₂, eluted with gradient of 0 to 100% MeOH inDCM). The product 14-9 was obtained as an amber oil (812 mg, 73%).

Preparation of Compound 14-10

To a solution of compound 14-9 in anhydrous acetonitrile (25 mL) andanhydrous DMF (3 mL), K₂CO₃ (821 mg, 4.39 mmol) and2-bromomethylphenylboronic acid (519 mg, 2.41 mmol) was added. Thereaction was stirred for 4 days at room temperature, filtered, and thefiltrate was concentrated in vacuo. Toluene was then added to theresidue and removed in vacuo to aid in removal of DMF,dilution-evaporation was repeated twice. The residue was dried underhigh vacuum and then purified by reversed-phase flash chromatography(C18 SiO₂, eluted with 0.1% TFA in MeCN). The pure product was isolatedby basification of combined and concentrated fractions with saturatedNaHCO₃, followed by triple extraction with DCM. The DCM portion was thendried over MgSO₄ and concentrated in vacuo to afford the title compound14-10 as a yellow residue (280 mg, 32%).

Preparation of Compound 14

A solution of compounds 14-10 (260 mg, 0.33 mmol) and 14-3 (448 mg, 0.99mmol) in ethanol (50 mL) was refluxed for 2 h. Then the reaction mixturewas allowed to cool down to room temperature and was concentrated invacuo. The residue was purified twice by reversed-phase flashchromatography (C18 SiO₂, eluted with MeCN and water). The pure productwas obtained as a pink/red solid (125 mg, 28%) after lyophilization.HPLC-MS: m/z 1176.9 (calcd. 1176.5 for M+H⁺); λ_(max)=655, 687 nm.

Preparation of Compound 15

Preparation of 7-(diethylamino)-2-phenyl-4H-1-benzopyran-4-one (15-1)

A mixture of N,N-diethyl-3-aminophenol (4.0 g, 24.2 mmol) and ethylbenzoylacetate (9.30 g, 48.4 mmol) was heated at 180° C. under argon for16 h. Then additional ethyl benzoylacetate (2.0 mL, 11 mmol) wasintroduced into the reaction mixture and it was stirred for 3 h followedby cooling to room temperature. The reaction mixture was diluted withethyl acetate (20 mL) followed by the addition of hexanes, whichproduced precipitate. The suspension was centrifuged, and thesupernatant was washed with 0.05 M HCl three times. The organic layerwas dried over MgSO₄, filtered, and concentrated in vacuo. The residuewas purified by flash chromatography (SiO₂, eluted with ethyl acetateand hexanes) to afford the compound 15-1 as a light yellow solid (773mg, 10%).

Preparation of 7-(diethylamino)-4-methyl-2-phenyl-1-benzopyryliumtetrafluoroborate (15-2)

A solution of compound 15-1 (773 mg, 2.6 mmol) in anhydrous THF (10 mL)was cooled to 0° C. under argon. Methylmagnesium bromide (1.2 mL, 3.6mmol) was added dropwise over 15 min. The flask was allowed to warm toroom temperature and stirred for 24 h. Then 48% tetrafluoroboric acid(1.4 mL, 10.7 mmol) was added and the mixture was stirred for 15 min.The solution was then diluted with DCM and washed with water. Theorganic layer was dried over MgSO₄, filtered, and concentrated in vacuo.The residue was purified by flash chromatography (C18 SiO₂, eluted withwater and MeOH). The fractions containing pure product were combined andconcentrated in vacuo to remove MeOH. The aqueous residue was thenextracted with DCM three times. Combined DCM layers were dried overMgSO₄, filtered, and concentrated in vacuo to yield compound 15-2 as amagenta solid (625 mg, 60%).

Preparation of Compound 15

A mixture of compounds 14-10 (100 mg, 0.12 mmol) and 15-2 (53.3 mg, 0.14mmol) in ethyl acetate (5 mL) was heated at 75° C. for 16 h. Thereaction mixture was concentrated in vacuo, and adsorbed on silica. Theimpurities were removed by washing the solids with a mixture of MeOH inDCM. The product was then recovered by sonicating the silica in DMSOfollowed by filtration. The filtrate was lyophilized to afford purecompound 15 (10 mg, 7%). HPLC-MS: m/z 1056 (calcd. 1056.6 for M⁺);λ_(max)=530 nm (broad).

Preparation of Compound 17

Preparation of (4-hydrazinylphenyl)acetic Acid Hydrochloride (17-1)

A mixture of 4-aminophenylacetic acid (6.86 g, 45.3 mmol) and HCl (12 M,100 mL) was refluxed for 15 min. After heating, the solution was cooledto −5° C. and aqueous NaNO₂ (25 mL) was added dropwise over 10 min at 0°C. After stirring the reaction mixture for 20 min, SnCl₂ in HCl (12 M,50 mL) was added dropwise over 10 min keeping the temperature below 0°C. The reaction mixture was then stirred for additional 2 h before itwas filtered and the precipitate was washed with cold water (100 mL),cold ethanol (200 mL), and diethyl ether (50 mL). The solid was thendried under high vacuum to yield compound 17-1 as a beige solid (6.68 g,73%).

Preparation of 2,3,3-trimethyl-3H-indole-5-acetic Acid (17-2)

A mixture of compound 17-1 (6.6 g, 32.5 mmol), acetic acid (80 mL),potassium acetate (6.39 g, 65.1 mmol), and isopropylmethyl ketone (8.41g, 10.5 mmol) was refluxed for 3 h and then cooled to room temperature.The solution was then concentrated in vacuo. The residue was dissolvedin DCM and washed with brine, then dried over MgSO₄, filtered, andconcentrated in vacuo. The resulting solid was purified by flashchromatography (SiO₂, eluted with 0 to 15% gradient of MeOH in DCM)yielding compound 17-2 as a light pink solid (4.9 g, 59%).

Preparation of Compound 17-3

A mixture of compound 17-2 (2.0 g, 7.8 mmol),N-(3-aminopropyl)methacrylamide hydrochloride (1.67 g, 9.39 mmol), HOBt(1.26 g, 9.39 mmol), EDC (2.25 g, 11.7 mmol), and triethylamine (3.39mL, 23.5 mmol) in DCM (30 mL) was stirred at room temperature for 16 hand then concentrated in vacuo. The residue was purified by flashchromatography (SiO₂, eluted with MeOH and DCM) affording compound 17-3(3.0 g, quant.).

Preparation of Compound 17-4

A solution of compound 17-3 (3.0 g, 8.7 mmol) and 1,3-propanesultone(7.7 mL, 87.8 mmol) in anhydrous acetonitrile (50 mL) was heated to 50°C. for 4 d. Then the reaction mixture was concentrated in vacuo to 10mL. The concentrate was then diluted into with ether/acetone (40 mL)producing copious precipitate. The slurry was centrifuged and thesupernatant was discarded. The solid was washed with acetone and driedin vacuo to yield compound 17-4 as a purple foam (3.5 g, 85%).

Preparation of Compound 17-10

A mixture of aldehyde 14-8 (250 mg, 0.63 mmol), 2-[(methylamino)methyl]phenylboronic acid (420.8 mg, 2.5 mmol) and triethylamine (0.367mL, 2.5 mmol) in DCM (40 mL) and DMF (8 mL) was heated to reflux for 3days. The reaction mixture was washed with water three times. The DCMlayer was loaded onto silica column and eluted with gradient of 0-15%MeOH in DCM. The product 17-10 was obtained as a crude yellow oil (320mg, 89%).

Preparation of Compound 17

A mixture of compounds 17-10 (318 mg, 0.56 mmol) and 17-4 (637 mg, 1.4mmol) in ethanol (50 mL) was refluxed for 16 h. Then the reaction wasconcentrated in vacuo and the residue was purified by reversed-phaseflash chromatography (C18 SiO₂, gradient elution with 0.25% HCl (aq) inMeOH). The product was isolated by basification of combined andconcentrated pure fractions with saturated NaHCO₃, followed by tripleextraction with DCM. The DCM portion was then dried over MgSO₄ andconcentrated in vacuo to afford the title compound 17 after triturationwith diethyl ether (150 mg, 26%) as a dark red solid. HPLC-MS: m/z1006.6 (calcd. 1006.5 for M+H⁺); λ_(max)=525 nm (broad).

Preparation of Compound 18

Preparation of 1-(5-carboxypentyl)-4-methylquinolinium Bromide (18-1)

A mixture of lepidine (2.0 mL, 14.7 mmol) and 6-bromohexanoic acid (4.33g, 22.2 mmol) was heated at 120° C. for 5 h and then at 130° C. for 16h. The reaction mixture was then cooled to room temperature andsonicated with acetone for 15 min. The supernatant was decanted and thesolid residue was additionally washed twice with fresh acetone undersonication yielding the compound 18-1 as a fine gray solid (2.4 g, 76%).

Preparation of Compound 18-2

In a dry 100 mL-flask compound 18-1 (1.0 g, 2.9 mmol) was dissolved in3:1 DCM/DMF (50 mL) followed by the addition ofN-(3-aminopropyl)methacrylamide hydrochloride (633 mg, 3.5 mmol), HOBt(598 mg, 4.4 mmol), EDC (849 mg, 4.4 mmol), and thriethylamine (0.857mL, 5.9 mmol). The reaction mixture was stirred at room temperature for16 h, followed by dilution with diethyl ether. The resulting suspensionwas centrifuged and the supernatant was discarded. The solid residue waspurified by flash chromatography (SiO₂, eluted with MeOH and DCM)affording target compound 18-2 as a pink-red amorphous solid (884 mg,65%).

Preparation of Compound 18

A mixture of compounds 17-10 (100 mg, 0.17 mmol) and 18-2 (200 mg, 0.43mmol) in ethanol (10 mL) was refluxed for 5 h. Then the reaction mixturewas cooled down to room temperature, and concentrated in vacuo. Theresidue was purified by flash chromatography (SiO₂, eluted with 0 to 30%gradient of MeOH in DCM, followed by 100% MeOH with 0.1% TFA). Theresulting yellow oil was re-purified with same method. The pure productwas dissolved in DCM and the solution was washed with saturated NaHCO₃,dried over anhydrous MgSO₄, filtered, and concentrated in vacuo. Purecompound 18 was obtained as an orange amorphous solid (9 mg, 5%).HPLC-MS: m/z 924.8 (calcd. 924.5 for M⁺); λ_(max)=380 nm (broad).

Preparation of Compound 35

Preparation of 2-bromo-9,10-dimethylanthracene (35-2)

In a 4-neck 10 L flask, 2-bromoanthraquinone (compound 35-1, 500 g, 1.74mole) was dissolved in anhydrous THF (6.5 L). The solution was cooled to−78° C. under nitrogen atmosphere and MeLi (2.39 L, 3.83 mole) was addeddropwise over 2 h. The darkened reaction mixture was stirred for another1 h at −78° C. and then was allowed to reach room temperature overnight.The reaction was quenched with saturated NH₄Cl (1.5 L). The organiclayer was separated, washed with H₂O, dried over anhydrous Na₂SO₄, andconcentrated under reduced pressure. The resulting yellow solid was thendissolved in MTBE (3.4 L). A solution of SnCl₂.2H₂O (2.12 kg, 9.40 mole)in concentrated HCl (1.67 L) was added under ice bath cooling over 30min. The reaction mixture was stirred for 3 h at room temperature, thentransferred to a separatory funnel, washed with H₂O, dried overanhydrous sodium sulfate, and concentrated under reduced pressure. Theresidue was purified by column chromatography (SiO₂, eluent: petroleumether/DCM 20:1) to give the title compound 35-2 (220 g, 44%) as a yellowsolid.

Preparation of 2-bromo-9,10-bis(bromomethyl)anthracene 35-3

A mixture of 2-bromo-9,10-dimethylanthracene 35-2 (6.89 g, 24.6 mmol)and N-bromosuccinimide (9.46 g, 53.15 mmol, 2.2 eq) in1,2-dichloroethane (100 mL) was refluxed for 2 h. The solvent wasremoved in vacuo, and the residue was triturated with methanol (100 mL),filtered, rinsed thoroughly with methanol, and dried to give compound35-3 as a yellow-orange solid (10.14 g, 95%).

General Procedure XI. Hydrolysis of bis-(bromomethyl)anthracenes.Preparation of 2-bromo-9,10-bis(hydroxymethyl)anthracene 35-4

A mixture of 2-bromo-9,10-bis(bromomethyl)anthracene 35-3 (22.9 g, 51.7mmol) and anhydrous calcium carbonate (31.02 g, 310.2 mmol, 6 eq) in 2:11,4-dioxane/H₂O (250 mL) was stirred under reflux for 20 h. The reactionwas then concentrated to remove dioxane, acidified with 1 M HCl (50 mL)and filtered. The collected solid was rinsed with water (3×50 mL), anddried under high vacuum yielding the product 35-4 as an orange-yellowsolid (15.0 g, 92%).

Preparation of 2-bromoanthracene-9,10-dicarbaldehyde 35-5

Dess-Martin periodinane (3.3 g, 7.88 mmol) was added to a solution of35-4 (1 g, 3.15 mmol) in 1:1 THF/DCM (250 mL) at 0° C. under nitrogen.The solution was stirred at room temperature for 3 h, then filtered, anddiluted with saturated NaHCO₃. Resulting mixture was transferred to aseparatory funnel and extracted with DCM three times. Combined DCMlayers were dried over MgSO₄ and concentrated in vacuo. The residue waspurified by flash chromatography (SiO₂, eluent: 100% DCM) affording 35-5as an orange solid (440 mg, 44%).

Preparation of2-bromo-9,10-bis[(3-methacrylamidopropyl)aminomethyl]anthracene 35-6

In a 1 L flame dried flask a mixture of APMA.HCl (5.75 g, 33.3 mmol) andDIPEA (5.8 mL, 33.3 mmol) in anhydrous THF (500 mL) was sonicated for 30min. Then anhydrous DMSO was added until a clear solution was obtained(ca. 20 mL). Glacial acetic acid (0.48 mL, 8.3 mmol) and dialdehyde 35-5(1.3 g, 4.2 mmol) were added to the solution, followed by stirring atroom temperature for 45 min. Sodium triacetoxyborohydride (9.3 g, 44.4mmol) was added in four equal portions over 2 h and the reaction mixturewas stirred at room temperature for 16 h. The reaction mixture was thenconcentrated in vacuo, diluted with DCM and saturated NaHCO₃ andtransferred to a separatory funnel. The aqueous layer was extracted withDCM 5 times. Combined DCM layers were then dried over MgSO₄ andconcentrated in vacuo. The residue was purified by reversed-phase flashchromatography (C18 SiO₂, gradient elution with 0.25% HCl (aq) in MeOH).The pure product was obtained by lyophilization (0.29 g, 11%) as a paleyellow solid.

General Procedure XII. Pd-Catalyzed Borylation of Aryl Bromides.Preparation of{2-[9,10-bis(3-methacrylamidopropyl)aminomethyl]anthracene}boronic Acid35-7

A mixture of diamine 35-6 (2 g, 3.53 mmol), bis(pinacolato)diboron (1.8g, 7.07 mmol), potassium acetate (2.1 g, 21.2 mmol), and Pd(dppf)Cl₂ waspurged 5 times with dry argon. Then anhydrous DMSO (120 mL) was addedand the reaction mixture was stirred at 50° C. under argon for 16 h.After consumption of the starting material, the reaction mixture wasdiluted with DCM (350 mL) and water (350 mL), stirred at roomtemperature for 20 minutes before transferring to a separatory funnel.The organic layer was discarded and the aqueous layer was additionallywashed with DCM 4 times. Remaining aqueous layer was concentrated invacuo and used for reversed-phase flash chromatography (C18 SiO₂, elutedwith gradient of 0.09% HCl (aq) in MeOH). The pure product was collectedby lyophilization to yield boronic acid 35-7 as a yellow-orange solid(558 mg, 30%).

Preparation of4-{[9,10-bis(3-methacrylamidopropyl)aminomethyl]anthr-2-yl}-2,2′-bipyridine35-8

In a flame dried 50-mL 3-neck flask fitted with a condenser, a mixtureof anthraceneboronic acid 35-7 (522 mg, 0.985 mmol),4-bromo-2,2′-bipyridine (154 mg, 0.657 mmol), and cesium carbonate (640mg, 1.97 mmol) in EtOH (15 mL) and water (2 mL) was degassed byrefluxing under argon stream for 75 minutes. Then Pd(OAc)₂ (29.7 mg,0.131 mmol) and PPh₃ (138 mg, 0.526 mmol) were added in one portion.Refluxing under argon was continued until the reaction was complete in90 minutes. The reaction mixture was then allowed to cool to roomtemperature and filtered; the solid residue was rinsed with DCM andMeOH. The filtrate was concentrated in vacuo, and the resulting residuewas purified by reversed-phase flash chromatography (C18 SiO₂, elutedwith gradient of 0.09% HCl in MeOH). The pure product was isolated bybasification of combined and concentrated fractions with solid NaHCO₃(200 mg) followed by extraction with DCM twice. The combined DCM layerswere then dried over MgSO₄ and concentrated in vacuo to yield product asa yellow solid (316 mg, 50%).

Preparation ofbis(2,2′-bipyridine)-4-{[9,10-bis(3-methacrylamidopropyl)aminomethyl]-anthr-2-yl}-2,2′-bipyridinerutheniumbis(hexafluorophosphate) 35-9

To a degassed solution of diamine 35-8 (75 mg, 0.117 mmol) in EtOH (20mL), Ru(bpy)₂Cl₂.2H₂O (57 mg, 0.117 mmol) was added and the reaction wasrefluxed under argon stream at 80° C. for 20 h, at which point thereaction was complete. The solvent was removed in vacuo, and the residuewas purified by reversed-phase flash chromatography (C18 SiO₂, elutedwith gradient of 0.09% HCl (aq) in acetonitrile). Combined fractionswith pure product were concentrated in vacuo to remove acetonitrile. Theproduct was then precipitated by addition of saturated solution ofammonium hexafluorophosphate (0.25 mL), collected by filtration, rinsedwith water and diethyl ether, and dried in vacuo. Yield: 159 mg(quant.).

Preparation of Compound 35

A mixture of intermediate 35-9 (409 mg, 0.30 mmol) and K₂CO₃ (415 mg, 3mmol) in anhydrous DMF (4 mL) was stirred at room temperature for 16 hunder argon. 2-Bromomethylphenylboronic acid (259 mg, 1.2 mmol) was thenadded and the reaction mixture was stirred at room temperature for 4 h.The reaction mixture was separated with reversed-phase flashchromatography (C18 SiO₂, eluted with gradient of 0.09% HCl (aq) inacetonitrile). Combined fractions with pure product were concentrated invacuo to remove acetonitrile. The product was then precipitated byaddition of saturated solution of ammonium hexafluorophosphate (0.25 mL)to the aqueous solution, and collected by centrifuging. The supernatantwas discarded and the precipitate was additionally washed with diethylether three times affording the title compound as an orange-red to darkred solid (123 mg, 65%). HPLC-MS: m/z 661.7 (calcd. 668.8 for M⁺²);λ_(max)=465 nm (broad).

Preparation of Compound 19

The intermediate 19-4 was synthesized following published protocol (Cui,J.; Jin, J.; Hsieh, Y.-H.; Yang, H.; Ke, B.; Damera, K.; Tai, P. C.;Wang, B. ChemMedChem 2013, 8 (8), 1384-1393).

General Procedure XIII. TBDMS Protection. Preparation of Compound 19-5

A solution of diol 35-4 (81 g, 0.256 mol), tert-butyldimethylsilylchloride (154 g, 1.02 mol), and imidazole (69.5 g, 1.02 mol) inanhydrous DCM (900 mL) was stirred for 3 h under argon. The reactionmixture was then filtered, and the filtrate was concentrated underreduced pressure to ˜200 mL. The concentrate was passed through a silicaplug (eluent: EtOAc/hexanes=1:1). Fractions containing main product(assessed by TLC) were collected and concentrated under reducedpressure. The residue was additionally purified by flash chromatography(SiO₂, eluent: gradient from 0 to 10% DCM in hexanes) to affordintermediate 19-5 (60 g, 43%) as a yellow solid.

Compound 19-6 was synthesized from intermediates 19-4 and 19-5,following the general procedure X.

General Procedure XIV. Double Amination of Anthracene Diol Via DibromideFormation. Preparation of Compound 19-7

To a solution of diol 19-6 (560 mg, 1.11 mmol) in anhydrous DCM (100mL), phosphorus tribromide (0.27 mL, 2.8 mmol) was added, and themixture was stirred at room temperature for 15 min. Then the solvent wasremoved under reduced pressure. The residue was resuspended in anhydrousMeCN (10 mL) and transferred to a slurry of APMA.HCl (597 mg, 3.3 mmol)and K₂CO₃ (1.32 g, 6.7 mmol) in a mixture of anhydrous MeCN and DCM 1:1(30 mL) that was pre-stirred at room temperature for at least 24 h. Thereaction mixture was stirred for 2-16 h and then filtered. The filtratewas concentrated under reduced pressure, and the residue was purified byreversed phase flash chromatography (C18 SiO₂, eluted with gradient ofMeOH in water+0.25% HCl) affording the title compound 19-7 (134 mg, 22%yield).

Compound 19 was synthesized from intermediate 19-7, following thegeneral procedure V. HPLC-MS: m/z 1020.5 (calcd. 1019.5 for M⁺);λ_(max)=565 nm. ¹H NMR (400 MHz, MeOH-d₄) δ ppm 8.62 (d, J=9.7 Hz, 1H),8.56 (t, J=8.0 Hz, 1H), 8.32 (dd, J=7.1, 2.9 Hz, 1H), 7.63-7.72 (m, 2H),7.49-7.59 (m, 2H), 7.23-7.33 (m, 8H), 7.17-7.23 (m, 2H), 7.10 (d, J=2.3Hz, 2H), 7.00 (dd, J=9.6, 2.2 Hz, 2H), 5.37 (s, 1H), 5.26 (s, 1H), 5.20(quin, J=1.5 Hz, 1H), 5.13 (quin, J=1.5 Hz, 1H), 4.80 (br. s., 2H), 4.73(br. s., 2H), 4.59 (s, 2H), 4.00 (s, 2H), 3.79 (s, 2H), 3.36 (s, 12H),3.06 (t, J=6.7 Hz, 2H), 2.89 (t, J=6.8 Hz, 2H), 2.70 (t, J=7.6 Hz, 2H),2.55 (t, J=7.4 Hz, 2H), 1.92-1.97 (m, 2H), 1.88-1.92 (m, 2H), 1.73 (dd,J=1.6, 1.0 Hz, 3H), 1.65 (dd, J 1.6, 1.0 Hz, 3H).

Preparation of Compound 20

Intermediate 20-2 was prepared by analogy with published procedure (Cui,J.; Jin, J.; Hsieh, Y.-H.; Yang, H.; Ke, B.; Damera, K.; Tai, P. C.;Wang, B. ChemMedChem 2013, 8 (8), 1384-1393).

Compound 20 was synthesized from intermediates 20-2 and 19-5, followinggeneral procedures X, XIV, and V. HPLC-MS: m/z 1066.1 (calcd. 1065.5 forM⁺); λ_(max)=700 nm.

Preparation of Compound 21

Intermediate 21-2 was synthesized from intermediates 19-5 and 11-3following the general procedures X and XIV.

General Procedure XV. Alkylation with MIDA Boronate Followed byDeprotection. Preparation of Compound 21

Solution of the diamine 21-2 (1.5 g, 1.65 mmol), DIPEA (0.99 mL, 5.68mmol), and 2-(bromomethyl)phenylboronic acid MIDA ester (1.7 g, 5.1mmol) in a mixture of anhydrous DCM and acetonitrile (20 mL:20 mL) wasstirred at ambient temperature for 1 h. Then the solvent was removedunder reduced pressure, the residue was dissolved in MeOH (25 mL), andtreated with 2M aqueous Na₂CO₃ (15 mL). The mixture was stirredvigorously for 2 h. Then the suspension was filtered and rinsed withMeOH (150 mL). The filtrate was concentrated under reduced pressure, andthe residue was partitioned between saturated NaHCO₃ (100 mL) and DCM(50 mL). The layers were separated and the aqueous layer wasadditionally extracted with DCM (3×30 mL). Combined DCM layers weredried over anhydrous Na₂SO₄, filtered, and concentrated under reducedpressure. The residue was purified by reversed phase flashchromatography (C18 SiO₂, eluted with 35% to 100% gradient of MeOH inwater+0.05% TFA). Yield: 747 mg (39% yield as mono-TFA salt) as darkblue solid. HPLC-MS: m/z 1062.4 (calcd. 1061.6 for M⁺). UV/Vis:λ_(max)=660 nm. ¹H NMR (400 MHz, MeOH-d₄) δ ppm 0.67 (s, 3H) 0.86 (br.s., 3H) 1.67 (s, 3H) 1.69-1.73 (m, 2H) 1.74 (s, 3H) 1.85-2.00 (m, 2H)2.61 (t, J=7.18 Hz, 2H) 2.70-2.78 (m, 2H) 2.93 (t, J=7.10 Hz, 2H) 3.08(t, J=6.51 Hz, 2H) 3.37 (s, 12H) 3.86 (br. s., 2H) 4.06 (br. s., 2H)4.56 (br. s., 2H) 4.84 (br. s., 2H) 5.15 (s, 1H) 5.21 (s, 1H) 5.29 (s,1H) 5.38 (s, 1H) 6.67 (dd, J=9.50, 2.50 Hz, 2H) 6.83-6.97 (m, 1H) 7.10(m, J=9.60 Hz, 1H) 7.19 (d, J=9.40 Hz, 2H) 7.24 (d, J=7.91 Hz, 1H)7.26-7.34 (m, 4H) 7.37 (d, J=8.64 Hz, 1H) 7.42 (d, J=7.06 Hz, 1H) 7.47(d, J=2.50 Hz, 2H) 7.51 (br. s., 1H) 7.61-7.70 (m, 2H) 8.43 (d, J=9.01Hz, 1H) 8.48-8.60 (m, 2H).

Preparation of Compound 49

Intermediate 49-1 was synthesized following published procedure [ref:Koide, et al. J. Am. Chem. Soc., 134 (11), 5029-5031].Compound 49 was synthesized from intermediate 49-1 and 19-5, followingsequence of general procedures X, XIV, and XV. HPLC-MS: m/z 1086.2(calcd. 1085.6 for M⁺). UV/Vis: λ_(max)=705 nm.

Preparation of Compound 45

Intermediate 45-1 was synthesized from commercially available startingmaterials by analogy with 49-1, as described in literature (Koide, Y.;Urano, Y.; Hanaoka, K.; Piao, W.; Kusakabe, M.; Saito, N.; Terai, T.;Okabe, T.; Nagano, T. J. Am. Chem. Soc. 2012, 134 (11), 5029-5031).Compound 45 was synthesized from intermediates 45-1 and 19-5, followinggeneral procedures X, XIV, and XV. HPLC-MS: m/z 1114.3 (calcd. 1113.6for M⁺). UV/Vis: λ_(max)=690 nm.

Preparation of Compound 48

Silaxanthone 48-1 was synthesized from commercially available startingmaterials by analogy with 49-1, as described in literature (Koide, Y.;Urano, Y.; Hanaoka, K.; Piao, W.; Kusakabe, M.; Saito, N.; Terai, T.;Okabe, T.; Nagano, T. J. Am. Chem. Soc. 2012, 134 (11), 5029-5031).Compound 48 was synthesized from silaxanthone 48-1 and bromoanthracene19-5, following general procedures X, XIV, and XV. HPLC-MS: m/z 1194.3(calcd. 1193.7 for M⁺). UV/Vis: λ_(max)=740 nm.

Preparation of Compound 56

Intermediate 56-1 was synthesized from commercially available startingmaterials by analogy with 49-1, as described in literature (Koide, Y.;Urano, Y.; Hanaoka, K.; Piao, W.; Kusakabe, M.; Saito, N.; Terai, T.;Okabe, T.; Nagano, T. J. Am. Chem. Soc. 2012, 134 (11), 5029-5031).

General Procedure XVI. Preparation of Silicon Rosamine Fluorophore ViaLithium-Halogen Exchange with t-BuLi and TMEDA. Preparation of Compound56-2

A solution of aryl bromide 19-5 (142 mg, 0.26 mmol) and TMEDA (0.02 mL,0.13 mmol) in anhydrous THF (4 mL) was cooled to −78° C. under argon. Asolution of tert-butyllithium in pentane (c=1.52 M, 0.19 mL, 0.29 mmol)was added dropwise and the mixture was stirred at −78° C. for 5-15 min,followed by rapid addition of silaxanthone 56-1 as a solution inanhydrous THF (c=0.075 M, 2.65 mL, 0.20 mmol). The mixture was stirredat −78° C. for 5-30 min and then was allowed to warm up to roomtemperature. After 1 h, the reaction was quenched with half-saturatedNH₄Cl, acidified with 0.1 M HCl (1 mL) and extensively extracted withDCM until aqueous layer was colorless. Combined organic layers weredried over anhydrous Na₂SO₄, filtered and concentrated under reducedpressure. The residue was purified by flash chromatography (SiO₂, elutedwith gradient from 2% to 25% MeOH in DCM) yielding bis-TBDMS diether56-2 (83 mg, 27% yield, 56% b. r. s. m.) as a dark-blue solid.

General Procedure XVIIA. Double Amination of TBDMS Diether. Preparationof Compound 56-3

A solution of intermediate 56-2 (83 mg, 0.09 mmol) in anhydrous DCM (9mL) was treated with 1 M thionyl chloride in DCM (0.5 mL, 0.5 mmol) for16 h at room temperature. Then the solvent was removed in vacuo and theresidue was rigorously dried under high vacuum to remove traces ofthionyl chloride. This was dissolved in anhydrous MeCN (5 mL) andtransferred to a slurry of APMA.HCl (330 mg, 1.85 mmol) and K₂CO₃ (511mg, 3.7 mmol) in anhydrous MeCN (50 mL) that was pre-stirred at roomtemperature for at least 24 h. To the suspension NaI (8 mg, 0.05 mmol)was added, and the mixture was stirred at room temperature for 2 h andthen filtered. Filtrate was concentrated in vacuo and the residue waspurified by reversed phase flash chromatography (C18 SiO₂, eluted withgradient from 5% to 100% MeOH in water+0.05% TFA). Yield: 9 mg (10%) asblue oil.

Compound 56 was synthesized from intermediate 56-3 following generalprocedure XV. HPLC-MS: m/z 1114.3 (calcd. 1113.6 for M⁺). UV/Vis:λ_(max)=665 nm.

Preparation of Compound 36

Preparation of Compound 36-1

A mixture of methyl 2-bromo-3-methylbenzoate (10 g, 43 mmol),pinacolborane (9.7 mL, 66 mmol), triethylamine (19 mL, 131 mmol), S-Phos(1.4 g, 3.5 mmol), and Pd(MeCN)Cl₂ (15.7 mg, 0.9 mmol) in degasseddioxane (200 mL) was heated at 60° C. under argon for 16 h. The reactionmixture was then filtered and concentrated under reduced pressure. Theresidue was purified by flash chromatography (SiO₂, eluted with gradientfrom 0% to 100% DCM in hexanes) affording the title compound 36-1 (11.2g, 94% yield) as a white solid.

Preparation of Compound 36-2

A mixture of intermediate 36-1 (11.2 g, 40 mmol), N-bromosuccinimide(7.8 g, 44 mmol), AIBN (10 mg, 0.06 mmol) in 1,2-dichloroethane (180 mL)was refluxed for 16 h. Then the reaction mixture was concentrated underreduced pressure. The residue was triturated with cold (4° C.) EtOAc andinsoluble solid was discarded. Solvent was removed under reducedpressure and the residue was purified by flash chromatography (SiO₂,eluted with gradient from 0% to 100% DCM in hexanes). This affordedtitle compound 36-2 (10.2 g, 72% yield) as a white solid.

Preparation of Compound 36-3

Solution of intermediate 36-2 (5.0 g, 14 mmol) in toluene (25 mL) wascooled to 0° C. under argon. Diisobutylaluminium hydride (c=1 M in THF,29.5 mL, 29.5 mmol) was added dropwise over 30 min. The mixture waspartitioned and the aqueous layer was exhaustively extracted with EtOAc.Combined organic layers were dried over anhydrous MgSO₄, filtered, andconcentrated under reduced pressure. The residue was purified by flashchromatography (SiO₂, eluted with gradient from 0% to 10% MeOH in DCM).This afforded title compound 36-3 (2.2 g, 69%) as a colorless oil.

Compound 36 was prepared form intermediate 21-2 and 36-3 following thegeneral procedure V. HPLC-MS: m/z 1086.4 (calcd. 1085.6 for M⁺). UV/Vis:λ_(max)=660 nm.

Preparation of Compound 37

Intermediate 37-1 was synthesized following the published procedure(Colvin, et al., PCT Int. Appl. (2008), WO 2008066921 A2 Jun. 5, 2008).

Compound 37 was prepared from intermediates 21-2 and 37-1 following thegeneral procedure V. HPLC-MS: m/z 1326.2 (calcd. 1325.5 for M⁺). UV/Vis:λ_(max)=660 nm.

Preparation of Compound 46, 47, 51, 52, 53, 55, 57, 58, 60

General Procedure XVIII. Protection of Boronic Acids with NeopentylGlycol. Preparation of Compound 51-1

A mixture of 4-cyano-2-methylphenylboronic acid (906 mg, 5.6 mmol),2,2-dimetyl-1,3-propanediol (641 mg, 6.15 mmol) and 3 Å molecular sieves(1 g) in anhydrous toluene (10 mL) was heated at 120° C. for 1 h andthen was allowed to cool to room temperature. The mixture was filteredand the filtrate was concentrated in vacuo. The residue was purified byflash chromatography (SiO₂, eluted with gradient from 20% to 60% EtOAcin hexanes). Yield: 1.054 g (82%) as yellowish solid.

General Procedure XIX. Radical Bromination. Preparation of Compound 51-2

A mixture of 4-cyano-2-methylphenylboronic acid neopentyl glycol ester51-1 (229 mg, 1.0 mmol), N-bromosuccinimide (208 mg, 1.17 mmol), andAIBN (22 mg, 0.13 mmol) in CCl₄ (20 mL) was refluxed for 20-30 min. Theprogress was monitored by TLC (DCM:hexane=6:4). The reaction mixture wasthen filtered and the filtrate was concentrated under reduced pressure.The residue was purified by flash chromatography (SiO2, eluted with 0%to 50% EtOAc in hexanes) affording the title compound 51-2 (312 mg,quant.) as a turbid oil which slowly crystallized upon storage at roomtemperature.

Compound 51 was prepared from intermediates 21-2 and 51-2 following thegeneral procedure V. The neopentyl glycol protecting group wasspontaneously removed during reversed phase purification. HPLC-MS: m/z1112.2 (calcd. 1111.6 for M⁺). UV/Vis: λ_(max)=660 nm. ¹H NMR (400 MHz,MeOH-d₄; mixture of two rotamers) δ ppm 8.53 (m, J=9.4 Hz, 2H),8.29-8.40 (m, 1H), 7.68-7.78 (m, 2H), 7.48-7.67 (m, 8H), 7.46 (d, J=2.7Hz, 2H), 7.18 (d, J=9.1 Hz, 2H), 6.70 (dd, J=9.7, 2.8 Hz, 2H), 5.43 (s,1H), 5.33 (s, 1H), 5.25 (quin, J=1.3 Hz, 1H), 5.18 (quin, J=1.3 Hz, 1H),5.06 (br. s., 2H), 4.96 (br. s., 2H), 4.23 (br. s., 2H), 4.03 (br. s.,2H), 3.37 (s, 12H), 3.12 (t, J 6.1 Hz, 2H), 2.98 (t, J=6.2 Hz, 2H), 2.88(dd, J=8.0, 6.6 Hz, 2H), 2.71 (dd, J=8.2, 6.6 Hz, 2H), 1.91-2.08 (m,4H), 1.77 (s, 3H), 1.69 (s, 3H), 0.82 (br. s., 3H), 0.63 (s, 3H).

Compounds 46, 47, 52, 53, 55, 57, 58, 60 were prepared from intermediate21-2 and corresponding boronic acid or neopentyl glycol boronatesfollowing general procedures XVIII, XIX, and V, as outlined in theScheme above.

For compound 46: HPLC-MS: m/z 1098.3 (calcd. 1097.6 for M⁺). UV/Vis:λ_(max)=660 nm.

For compound 47: HPLC-MS: m/z 1268.0 (calcd. 1267.3 for M⁺). UV/Vis:λ_(max)=660 nm.

For compound 52: HPLC-MS: m/z 1198.2 (calcd. 1197.5 for M⁺). UV/Vis:λ_(max)=660 nm. ¹H NMR (400 MHz, MeOH-d₄; mixture of two rotamers) δ ppm8.82 (s, 1H), 8.30 (d, J=7.9 Hz, 2H), 7.79-7.88 (m, 1H), 7.67-7.78 (m,2H), 7.45-7.67 (m, 6H), 7.39-7.45 (m, 3H), 6.98 (d, J=2.7 Hz, 2H), 6.78(dd, J=9.3, 2.7 Hz, 2H), 5.44 (s, 1H), 5.36 (s, 1H), 5.22 (quin, J=1.3Hz, 1H), 5.18 (quin, J=1.3 Hz, 1H), 5.03 (br. s, 2H), 4.25 (br. s., 2H),4.07 (br. s., 2H), 3.15 (t, J=6.6 Hz, 2H), 3.06 (t, J=6.6 Hz, 2H), 2.94(s, 12H), 2.72-2.83 (m, 2H), 2.67 (dd, J=9.3, 7.2 Hz, 2H), 1.99-2.08 (m,2H), 1.80 (s, 2H), 1.75 (s, 3H), 1.69 (s, 3H), 0.60 (s, 3H), 0.55 (s,3H).

For compound 53: HPLC-MS: m/z 1276.2 (calcd. 1275.6 for M⁺). UV/Vis:λ_(max)=660 nm. ¹H NMR (400 MHz, MeOH-d₄; mixture of two rotamers) δ ppm8.83 (s, 1H), 8.47 (br. s., 1H), 8.14-8.26 (m, 1H), 7.76 (d, J=7.8 Hz,1H), 7.60-7.73 (m, 6H), 7.48-7.54 (m, 2H), 7.36-7.47 (m, 3H), 6.98 (d,J=2.8 Hz, 2H), 6.81 (d, J=7.2 Hz, 2H), 5.48 (s, 1H), 5.41 (s, 1H), 5.25(quin, J=1.3 Hz, 1H), 5.21 (quin, J=1.3 Hz, 1H), 4.92 (br. s., 2H), 4.76(br. s., 2H), 4.29 (br. s, 2H), 4.17 (br. s., 2H), 3.16 (t, J=6.6 Hz,2H), 3.10 (t, J=6.6 Hz, 2H), 2.95 (s, 12H), 2.76-2.84 (m, 2H), 2.65-2.73(m, 2H), 2.64 (s, 6H), 2.48 (s, 6H), 2.00-2.11 (m, 2H), 1.82-1.90 (m,2H), 1.79 (s, 3H), 1.73 (s, 3H), 0.61 (s, 3H), 0.55 (s, 3H).

For compound 55: HPLC-MS: m/z 1276.1 (calcd. 1275.6 for M⁺). UV/Vis:λ_(max)=660 nm. ¹H NMR (400 MHz, MeOH-d₄; mixture of two rotamers) δ ppm8.83 (br. s., 1H), 8.54 (d, J=9.1 Hz, 1H), 8.48 (d, J=8.6 Hz, 1H),7.79-7.87 (m, 2H), 7.67-7.77 (m, 2H), 7.51-7.59 (m, 3H), 7.32-7.51 (m,3H), 7.42 (d, J=2.7 Hz, 2H), 7.18 (d, J=9.7 Hz, 2H), 6.66 (dd, J=9.7,2.5 Hz, 2H), 5.42 (s, 1H), 5.28 (s, 1H), 5.23 (s, 1H), 5.15 (s, 1H),5.06 (br. s., 2H), 4.64 (br. s., 2H), 4.31 (br. s., 2H), 4.03 (br. s.,2H), 3.34 (s, 12H), 3.08-3.19 (m, 2H), 2.95 (s, 6H), 2.88 (t, J=6.6 Hz,2H), 2.57-2.66 (m, 4H), 2.54 (s, 6H), 1.90-2.10 (m, 2H), 1.80-1.90 (m,2H), 1.75 (s, 3H), 1.65 (s, 3H), 0.80 (br. s., 3H), 0.66 (s, 3H).

For compound 57: HPLC-MS: m/z 1198.1 (calcd. 1197.5 for M⁺). UV/Vis:λ_(max)=660 nm. ¹H NMR (400 MHz, MeOH-d₄; mixture of two rotamers) δ ppm8.50-8.60 (m, 2H), 8.47 (d, J=9.1 Hz, 1H), 8.28 (t, J=9.6 Hz, 1H),7.58-7.75 (m, 5H), 7.50-7.57 (m, 2H), 7.47 (d, J=2.7 Hz, 2H), 7.36-7.49(m, 2H), 7.14 (d, J=9.5 Hz, 2H), 6.65 (dd, J=9.5, 2.7 Hz, 2H), 5.35 (s,1H), 5.27 (s, 1H), 5.19 (quin, J=1.2 Hz, 1H), 5.12 (quin, J=1.2 Hz, 1H),4.92 (br. s., 2H), 4.60 (br. s., 2H), 4.19 (br. s., 2H), 4.01 (br. s.,2H), 3.36 (s, 12H), 3.07 (t, J=6.6 Hz, 2H), 2.95 (t, J=6.6 Hz, 2H),2.74-2.83 (m, 2H), 2.61-2.74 (m, 2H), 1.87-2.03 (m, 2H), 1.73-1.82 (m,2H), 1.71 (s, 3H), 1.64 (s, 3H), 0.88 (br. s., 3H), 0.64 (s, 3H).

For compound 58: HPLC-MS: m/z 1152.3 (calcd. 1151.5 for M⁺). UV/Vis:λ_(max)=660 nm. ¹H NMR (400 MHz, MeOH-d₄; mixture of two rotamers) δ ppm8.85 (br. s., 1H), 8.28-8.40 (m, 2H), 8.24 (dd, J=8.4, 2.7 Hz, 2H), 7.88(d, J=8.4 Hz, 1H), 7.79 (d, J=9.1 Hz, 1H), 7.69-7.75 (m, 1H), 7.53-7.63(m, 2H), 7.43 (d, J=9.0 Hz, 2H), 7.34-7.52 (m, 3H), 6.98 (d, J=2.7 Hz,2H), 6.78 (dd, J=9.0, 2.7 Hz, 2H), 5.46 (s, 1H), 5.39 (s, 1H), 5.22(quin, J=1.3 Hz, 1H), 5.19 (quin, J=1.3 Hz, 1H), 4.94 (br. s, 4H,overlaps with CD₃OH signal), 4.27 (br. s, 2H), 4.13 (br. s., 2H), 3.17(t, J=6.6 Hz, 2H), 2.94 (s, 12H), 2.90-2.97 (m, 2H), 2.75-2.86 (m, 2H),2.66-2.75 (m, 2H), 2.00-2.12 (m, 2H), 1.78-1.90 (m, 2H), 1.76 (s, 3H),1.71 (s, 3H), 0.60 (s, 3H), 0.55 (s, 3H).

For compound 60: HPLC-MS: m/z 1122.2 (calcd. 1121.6 for M⁺). UV/Vis:λ_(max)=660 nm. ¹H NMR (400 MHz, MeOH-d₄; mixture of two rotamers) δ ppm8.50-8.61 (m, 2H), 8.39-8.50 (m, 1H), 7.58-7.69 (m, 2H), 7.45 (d, J=2.7Hz, 2H), 7.36-7.49 (m, 2H), 7.32 (d, J=8.9 Hz, 1H), 7.15 (m, J=8.4 Hz,3H), 6.84-6.93 (m, 2H), 6.75-6.83 (m, 2H), 6.65 (dd, J=9.7, 2.3 Hz, 2H),5.38 (s, 1H), 5.29 (s, 1H), 5.21 (quin, J 1.3 Hz, 1H), 5.14 (quin, J=1.3Hz, 1H), 4.73 (br. s., 2H), 4.54 (br. s., 2H), 3.87 (br. s, 2H), 3.75(s, 3H), 3.68 (br. s, 2H), 3.35 (s, 12H), 3.08 (t, J=6.5 Hz, 2H), 2.95(t, J 6.6 Hz, 2H), 2.93 (s, 3H), 2.65-2.71 (m, 2H), 2.57-2.65 (m, 2H),1.84-1.94 (m, 2H), 1.75 (s, 3H), 1.69-1.74 (m, 2H), 1.67 (s, 3H), 0.87(br. s, 3H), 0.63 (s, 3H).

Preparation of Compounds 39, 40, 43, 44

General Procedure XX. PEG Monomethacrylates. Preparation of Compound43-1

To a solution of mono-Boc-protected PEG₄ diamine (1.0 g, 2.97 mmol) inchloroform (30 mL), methacrylic anhydride (0.55 mL, 3.46 mmol) andtriethylamine (0.55 mL, 3.95 mmol) were successively added, and thereaction mixture was stirred at room temperature overnight. Then thereaction mixture was concentrated under reduced pressure and the residuewas taken up into EtOAc (40 mL). The solution was washed with 1 N HCl(2×40 mL), saturated NaHCO₃ (40 mL), and brine (40 mL). The organiclayer was dried over anhydrous Na₂SO₄, filtered, and concentrated underreduced pressure. The residue was purified by reversed phase flashchromatography (C18 SiO₂, eluted with gradient of MeOH in water+0.05%TFA) affording the desired intermediate (553 mg, 46% yield) as acolorless oil. The purified oil (553 mg, 1.37 mmol) was dissolved in DCM(5 mL) and treated with TFA (1 mL) for 3 h at room temperature, and thenthe reaction mixture was concentrated under reduced pressure. Theresidue was dried under high vacuum yielding desiredPEG₄-mono-methacrylamide 43-1 (750 mg, quant., TFA salt) as amber oil.Intermediates 39-1, 40-1, and 44-1 were prepared from correspondingmono-Boc-protected oligo(ethyleneglycol)diamines following the generalprocedure XX.

Compounds 39, 40, 43, and 44 were prepared from corresponding amines39-1, 40-1, 43-1, and 44-1, and common intermediate diol 21-1, followingthe general procedures XVIIA and XV, as outlined in the scheme above.

For compound 39: HPLC-MS: m/z 1210.5 (calcd. 1209.6 for M⁺). UV/Vis:λ_(max)=660 nm. ¹H NMR (400 MHz, DMSO-d₆) δ ppm 8.41-8.54 (m, 2H), 8.19(br. s., 1H), 7.60-7.67 (m, 1H), 7.51-7.60 (m, 2H), 7.47 (d, J=2.8 Hz,2H), 7.17-7.43 (m, 7H), 6.91-7.17 (m, 4H), 6.71 (dd, J=9.8, 2.7 Hz, 2H),5.52-5.59 (m, 1H), 5.54 (s, 1H), 5.18-5.29 (m, 2H), 4.67 (br. s., 2H),4.60 (br. s., 2H), 3.94 (br. s., 2H), 3.76 (br. s., 2H), 3.31-3.38 (m,8H), 3.29 (s, 12H), 3.22 (t, J=6.5 Hz, 2H), 3.12-3.19 (m, 8H), 3.10 (t,J=6.5 Hz, 2H), 2.69-2.77 (m, 2H), 2.58-2.64 (m, 2H), 1.75 (s, 3H), 1.74(s, 3H), 0.69 (s, 3H), 0.61 (s, 3H).

For compound 40: HPLC-MS: m/z 1297.7 (calcd. 1298.5 for M⁺). UV/Vis:λ_(max)=660 nm.

For compound 43: HPLC-MS: m/z 1386.5 (calcd. 1385.8 for M⁺). UV/Vis:λ_(max)=660 nm.

For compound 44: HPLC-MS: m/z 1474.4 (calcd. 1473.8 for M⁺). UV/Vis:λ_(max)=660 nm.

Preparation of Compound 50

Intermediate 50-1 was prepared as described elsewhere (Suri, Jeff T. PCTInt. Appl., 2008014280, 31 Jan. 2008).

Compound 50 was prepared from intermediates 21-1 and 50-1, followinggeneral procedures XVIIA and V. The final compound was additionallypurified with reversed phase flash chromatography (C18 SiO₂, eluted withgradient of MeCN in 10 mM aqueous NH₄HCO₃). HPLC-MS: m/z 1385.0 (calcd.1385.5 for M⁺Na⁺). UV/Vis: λ_(max)=655 nm.

Preparation of Compound 23

Compound 23 was synthesized from aldehyde 14-9 following the combinationof general procedures VII and V as outlined in the scheme above.HPLC-MS: m/z 1057.0 (calcd. 1057.6 for M⁺). UV/Vis: λ_(max)=560 nm.

Preparation of Compound 22

Preparation of 5-bromo-2,3,3-trimethylindolenine 22-9

A solution of 4-bromophenyl hydrazine (10 g, 44.7 mmol),3-methyl-2-butanone (9.6 mL, 89.5 mmol) in anhydrous EtOH (160 mL), andconc. H₂SO₄ (5 mL) was refluxed for 1 h under argon. Then the reactionmixture was concentrated in vacuo to 80 mL, diluted with DCM, andtransferred to a separatory funnel. Aqueous layer was discarded, andorganic layer was washed three times with saturated NaHCO₃, water, andbrine. The DCM portion was then dried over MgSO₄ and concentrated invacuo to yield the title product (5.1 g, 48%).

Preparation of 5-bromo-1,2,3,3-tetramethyl-3H-indolium iodide 22-10

A mixture of intermediate 22-9 (5.1 g, 21.4 mmol) and iodomethane (3.96mL, 64.3 mmol) in acetonitrile (40 mL) was heated to 80° C. in apressure flask for 16 h producing light-yellow precipitate. The reactionmixture was allowed to cool to room temperature, diluted with diethylether and then cooled to −78° C. The product was collected byfiltration, and rinsed with cold diethyl ether yielding the titleproduct 22-10 (7.51 g, 93%).

Preparation of1,3,3-trimethyl-2-[4-(phenylamino)-1,3-butadien-1-yl]-3H-indolium Iodide22-12

A mixture of N-(3-phenylimino-1-propen-1-yl)aniline hydrochloride (1.61g, 6.2 mmol) and 1,2,3,3-tetramethyl-3H-indolium iodide (750 mg, 2.49mmol) in acetic anhydride (40 mL) was heated to 80° C. under argon for20 min. The reaction mixture was then diluted with DCM and transferredto a separatory funnel. The organic layer was washed with water andbrine, then dried over MgSO₄ and concentrated in vacuo. The crudeproduct was purified by flash chromatography (SiO₂, eluted with DCM andMeOH) yielding the title product 22-12 (439 mg, 41%).

Preparation of5-bromo-2-[(5-(1,3-dihydro-1,3,3-trimethyl-2H-indol-2-ylidene)-1,3-pentadien-1-yl]-1,3,3-trimethyl-3H-indoliumIodide 22-13

A mixture of sodium acetate (750 mg, 9.1 mmol), intermediates 22-12 (430mg, 0.911 mmol) and 22-10 (1.03 g mg, 2.72 mmol), and pyridine (2 mL) inacetic anhydride (16 mL) was stirred for 1 h. The reaction mixture wasdiluted with DCM and neutralized with saturated NaHCO₃. The mixture wasthen partitioned and the DCM layer was washed with brine 2 times. TheDCM portion was then dried over MgSO₄, and concentrated in vacuo. Crudeproduct was purified by flash chromatrography (SiO₂, eluted with DCM andMeOH) affording the title product 22-13 (311 mg, 58%).

Preparation of5-{[9,10-bis(3-methacrylamidopropyl)aminomethyl]anthr-2-yl}-2-[(5-(1,3-dihydro-1,3,3-trimethyl-2H-indol-2-ylidene)-1,3-pentadien-1-yl]-1,3,3-trimethyl-3H-indoliumIodide 22-14

To a mixture of intermediates 35-7 (200 mg, 0.339 mmol), 22-13 (215 mg,0.406 mmol), and cesium carbonate (331 mg, 1.01 mmol) in degassed EtOH(15 mL) and water (1 mL), palladium(II) acetate (7.6 mg, 0.034 mmol) andtriphenylphosphine (36 mg, 0.136 mmol) were added. The reaction mixturewas refluxed for 16 h under argon then concentrated in vacuo. Theresidue was dissolved in DCM and washed with saturated NaHCO₃ and brine.The DCM layer was dried over MgSO₄ and concentrated in vacuo. Crudeproduct was purified by reversed-phase flash chromatography (C18 SiO₂,eluted with gradient of 0.09% HCl in MeOH). The pure product wasisolated by basification of combined and concentrated fractions withsaturated NaHCO₃ followed by triple extraction with DCM. The combinedDCM layers were then dried over MgSO₄ and concentrated in vacuo to yieldthe title product 22-14 (92 mg, 27%).

Preparation of Compound 22

To a mixture of intermediate 22-14 (85 mg, 0.085 mmol) and K₂CO₃ (118mg, 0.85 mmol) in anhydrous acetonitrile (6 mL) and anhydrous DCM (4mL), 2-bromomethylphenylboronic acid (55 mg, 0.256 mmol) was added. Thereaction was stirred under argon at room temperature for 40 min, thenmore 2-bromomethylphenylboronic acid (36 mg, 0.168 mmol) was added withanhydrous MeOH (2 mL) and the resulting mixture was stirred for 2 h. Thereaction mixture was then concentrated in vacuo to 10 mL and filtered.The precipitate was additionally washed with DCM. The filtrate wasconcentrated in vacuo. The crude product was purified by reversed-phaseflash chromatography (C18 SiO₂, eluted with gradient of 0.09% HCl inMeOH). The pure product was isolated by basification of combined andconcentrated fractions with saturated NaHCO₃, followed by tripleextraction with DCM. The combined DCM layers were then dried over MgSO₄and concentrated in vacuo. The title compound 22 was precipitated byhexanes and dried in vacuo (55 mg, 51%). HPLC-MS: m/z 1135.3 (calcd.1135.6 for M⁺). UV/Vis: λ_(max)=660 nm.

Preparation of Compound 80

Compound 80 was synthesized from intermediates 35-7 and 22-13, followinggeneral procedures III, XII, III, and XV, as outlined in the schemeabove. HPLC-MS: m/z 1212.4 (calcd. 1211.7 for M+H⁺). UV/Vis: λ_(max)=650nm.

Preparation of Compound 24

Compound 24 was synthesized from intermediates 2-2 and 35-7, followinggeneral procedures III and V with K₂CO₃ instead of DIPEA as a base inthe last step. HPLC-MS: m/z 1352.6 (calcd. 1351.6 for M+H⁺). UV/Vis:λ_(max)=650 nm. ¹H NMR (400 MHz, DMSO-d₆; some integrals were broadenedand not resolved) δ ppm 8.66 (s, 2H), 8.59 (br. s., 1H), 8.55 (br. s.,2H), 8.44 (d, J=8.9 Hz, 1H), 8.36 (m, J=8.9 Hz, 1H), 7.70 (d, J=6.0 Hz,1H), 7.58-7.67 (m, 4H), 7.55 (m, J=8.3 Hz, 1H), 7.46-7.53 (m, 2H), 7.43(d, J=7.4 Hz, 1H), 7.30-7.41 (m, 6H), 7.20-7.30 (m, 3H), 7.09-7.20 (m,2H), 5.43 (br. s, 1H), 5.39 (br. s, 1H), 5.14 (quin, J=1.5 Hz, 1H), 5.10(quin, J=1.5 Hz, 1H), 4.50 (br. s., 4H), 3.95 (br. s., 2H), 3.78 (br.s., 2H), 2.80 (m, J=6.9 Hz, 4H), 2.19 (br. s., 4H), 1.68 (s, 3H),1.63-1.83 (m, 20H), 1.62 (s, 3H).

Preparation of Compound 78

Compound 78 was synthesized from intermediate 35-7, 3-bromophenol, andIR-780 following general procedures III, XV, and VIII, as outlined inthe scheme above. HPLC-MS: m/z 1350.7 (calcd. 1349.8 for M⁺). UV/Vis:λ_(max)=780 nm. ¹H NMR (400 MHz, MeOH-d₄) δ ppm 8.71 (br. s., 1H),8.43-8.55 (m, 1H), 8.38 (d, J=7.2 Hz, 2H), 8.11 (d, J=14.4 Hz, 2H), 7.76(d, J=9.4 Hz, 1H), 7.54-7.66 (m, 4H), 7.46-7.54 (m, 2H), 7.40-7.45 (m,1H), 7.36 (t, J=7.4 Hz, 2H), 7.33 (d, J=7.4 Hz, 2H), 7.26 (m, J=7.9 Hz,5H), 7.20-7.24 (m, 2H), 7.18 (t, J=7.1 Hz, 2H), 7.04-7.14 (m, 2H), 6.22(d, J=14.2 Hz, 2H), 5.35 (s, 1H), 5.31 (s, 1H), 5.14 (quin, J=1.3 Hz,1H), 5.15 (quin, J=1.3 Hz, 1H), 4.91 (br. s., 2H), 4.78 (br. s., 2H),4.20 (br. s., 2H), 4.08 (t, J=7.2 Hz, 4H), 3.84 (br. s., 2H), 3.01 (t,J=6.5 Hz, 2H), 3.04 (t, J=6.7 Hz, 2H), 2.80 (t, J=6.1 Hz, 4H), 2.71-2.78(m, 2H), 2.63 (dd, J=9.1, 6.1 Hz, 2H), 2.09 (quin, J=5.7 Hz, 2H),1.79-1.94 (m, 8H), 1.66 (s, 3H), 1.67 (s, 3H), 1.40 (s, 12H), 1.01 (t,J=7.4 Hz, 6H).

Preparation of Compound 79

Compound 79 was synthesized from intermediate 78-2 and IR-783 followinggeneral procedure VIII, as outlined in the scheme above. HPLC-MS: m/z769.5 (calcd. 769.4 for [M+H]²⁺). UV/Vis: λ_(max)=785 nm. ¹H NMR (400MHz, MeOH-d₄; an extra set of Cy7 signals was present in the spectrum) δppm 8.65 (br. s., 1H), 8.49 (d, J 8.6 Hz, 1H), 8.38-8.47 (m, 1H), 8.44(d, J=14.1 Hz, 2H), 8.14-8.26 (m, 1H), 8.10 (d, J=14.1 Hz, 2H), 7.79 (d,J=9.1 Hz, 1H), 7.64 (t, J=7.9 Hz, 1H), 7.52-7.61 (m, 4H), 7.51 (d, J=7.3Hz, 2H), 7.45-7.49 (m, 1H), 7.42 (t, J=7.5 Hz, 2H), 7.34-7.40 (m, 3H),7.22-7.34 (m, 11H), 7.16 (t, J=7.4 Hz, 4H), 6.33 (d, J=14.1 Hz, 2H),6.26 (d, J=14.1 Hz, 2H), 5.33 (s, 1H), 5.31 (s, 1H), 5.13 (s, 1H), 5.11(s, 1H), 4.97 (br. s., 2H), 4.31 (br. s., 2H), 4.22 (t, J=7.1 Hz, 4H),4.14 (t, J=6.3 Hz, 4H), 3.92 (br. s., 2H), 3.35 (s, 3H), 3.04 (t, J=6.2Hz, 2H), 3.01 (t, J=6.6 Hz, 2H), 2.88 (s, 12H), 2.79-2.83 (m, 4H), 2.76(t, J=5.6 Hz, 4H), 2.67 (m, J=8.4 Hz, 2H), 2.02-2.13 (m, 2H), 1.81-2.02(m, 22H), 1.71-1.77 (m, 12H), 1.65 (s, 3H), 1.64 (s, 3H), 1.39 (s, 12H)

Preparation of Compound 84

Aza-BODIPY monophenol 84-1 was prepared as described elsewhere (Jokic,T.; Borisov, S. M.; Saf, R.; Nielsen, D. A.; Ktihl, M.; Klimant, I.Anal. Chem. 2012, 84 (15), 6723-6730).

General Procedure XXI. Conversion of Phenols into Aromatic Triflates.Preparation of Compound 84-2

Solution of aza-BODIPY phenol 84-1 (250 mg, 0.49 mmol) and pyridine(0.08 mL, 1.0 mmol) in anhydrous DCM (8 mL) was cooled to −30° C. underargon atmosphere. Triflic anhydride (0.11 mL, 0.66 mmol) was added andthe reaction mixture was stirred at −30° C. for 30 min. Then thereaction mixture was quenched with 0.1 M HCl (5 mL) and saturated NH₄Cl(5 mL), diluted with water (10 mL) and partitioned with additional DCM(20 mL). Aqueous layer was discarded. Organic extract was washed withhalf-saturated NH₄Cl (20 mL), dried over anhydrous Na₂SO₄, filtered, andconcentrated under reduced pressure. The residue was purified by flashchromatography (SiO₂, eluted with gradient from 10% to 40% DCM inhexanes). Obtained the desired triflate 84-2 (228 mg, 72% yield) as adark-purple solid.

General Procedure XXII. Suzuki-Miyaura Coupling with Aromatic Triflates.Preparation of Compound 84-3

A mixture of aza-BODIPY triflate 84-2 (68 mg, 0.105 mmol), anthraceneboronic acid 35-7 (173 mg, 0.33 mmol), K₃PO₄ (134 mg, 0.63 mmol),Pd(OAc)₂ (5.6 mg, 0.025 mmol), and XantPhos (15 mg, 0.026 mmol) indegassed anhydrous THF (20 mL) was refluxed under argon atmosphere for16 h. Then the reaction mixture was cooled down to ambient temperature,filtered through Celite® (washed with MeOH), filtrate was concentrated,and the residue was purified by reversed-phase flash chromatography (C18SiO₂, eluted with gradient from 60% to 100% of MeOH in water+0.05% TFA).Obtained the desired product (11.6 mg, 11%) as a dark-blue solid.

Compound 84 was prepared from the intermediate 84-3, following thegeneral procedure XV. HPLC-MS: m/z 1251.4 (calcd. 1250.6 for M+H⁺).UV/Vis: λ_(max)=665 nm.

Preparation of Compound 85

Aza-BODIPY monophenol 85-1 was prepared as described elsewhere (Jokic,T.; Borisov, S. M.; Saf, R.; Nielsen, D. A.; Ktihl, M.; Klimant, I.Anal. Chem. 2012, 84 (15), 6723-6730).

Compound 85 was prepared from 85-1, following the general proceduresXXI, XXII, and XV, as outlined in the scheme above, by analogy with thepreparation of compound 85. HPLC-MS: m/z 1251.4 (calcd. 1250.6 forM+H⁺). UV/Vis: λ_(max)=660 nm.

Preparation of Compound 26

Compound 26 was prepared from 1,4-dibromobenzene and intermediates 11-3and 35-7 via general procedures X, III, and V as outlined in the schemeabove. HPLC-MS: m/z 1138.5 (calcd. 1137.6 for M⁺). UV/Vis: λ_(max)=650nm.

Preparation of Compound 27

Compound 27 was prepared from 1,4-dibromo-2,5-dimethylbenzene andintermediates 11-3 and 35-7 via general procedures X, III, and V asoutlined in the scheme above. HPLC-MS: m/z 1166.5 (calcd. 1165.6 forM⁺). UV/Vis: λ_(max)=655 nm.

Preparation of Compound 28

Preparation of Compound 28-1

A mixture of 6-diethylaminonaphth-1-ol (174 mg, 0.81 mmol) and4-bromobenzaldehyde (75 mg, 0.0.41 mmol) in neat triflic acid (2 mL) washeated in a closed vial at 105° C. for 2 h. Then the reaction mixturewas allowed to cool down to room temperature and diluted withDCM:water=1:1 (50 mL). The layers were separated and aqueous layer wasadditionally extracted with DCM (3×15 mL). Combined organic layers weredried over anhydrous Na₂SO₄, filtered and concentrated under reducedpressure. The residue was purified by reversed phase flashchromatography (C18 SiO₂, eluted with 80% MeOH in water+0.05% TFA).Yield: 50 mg (8.5%) as dark-blue powder.

Compound 28 was synthesized from intermediate 28-1 and 35-7 followingthe general procedures III and XV as outlined in the scheme above.HPLC-MS: m/z 1252.3 (calcd. 1251.7 for M⁺). UV/Vis: λ_(max)=685 nm.

Preparation of Compound 33

Intermediate 33-1 was synthesized as described in literature(Cherevatskaya, M. et al. Angew. Chem. Int. Ed., 51 (17), 4062-4066,2012).Compound 33 was synthesized form intermediates 33-1 and 35-7, followinggeneral procedures III and V, as outlined in the scheme above. HPLC-MS:m/z 1200.4 (calcd. 1199.6 for M⁺). UV/Vis: λ_(max)=585 nm. ¹H NMR (400MHz, CDCl₃) δ ppm 8.35 (d, J 9.3 Hz, 1H), 8.26 (d, J=8.8 Hz, 1H),7.70-7.85 (m, 3H), 7.59-7.68 (m, 4H), 7.51-7.58 (m, 2H), 7.31-7.51 (m,8H), 7.20 (s, 2H), 5.37 (s, 1H), 5.34 (s, 1H), 5.13 (s, 1H), 5.11 (s,1H), 4.58 (br. s., 2H), 4.53 (s, 2H), 3.94 (br. s., 2H), 3.58 (t, J=5.5Hz, 4H), 3.54 (t, J=5.5 Hz, 4H), 3.39-3.42 (m, 2H), 3.09 (t, J=6.3 Hz,4H), 2.82 (t, J=5.8 Hz, 4H), 2.57 (t, J=7.5 Hz, 2H), 2.48 (t, J=7.5 Hz,2H), 2.15 (quin, J=6.0 Hz, 4H), 2.00 (quin, J=6.0 Hz, 4H), 1.72 (s, 3H),1.70 (s, 3H), 1.56-1.64 (m, 2H), 1.45-1.54 (m, 2H), 1.21-1.31 (m, 4H).

Preparation of Compound 42

Compound 42 was synthesized form 1,3-diiodobenzene and intermediate 11-3following general procedures X, III, and XV, as outlined in the schemeabove. HPLC-MS: m/z 1138.3 (calcd. 1137.6 for M⁺). UV/Vis: λ_(max)=650nm. ¹H NMR (400 MHz, MeOH-d₄) δ ppm 8.39 (d, J=9.0 Hz, 1H), 8.36 (d,J=8.7 Hz, 1H), 8.22-8.33 (m, 2H), 7.89 (d, J=7.9 Hz, 1H), 7.71-7.84 (m,2H), 7.52-7.70 (m, 5H), 7.25-7.47 (m, 11H), 7.08-7.25 (m, 3H), 6.97 (d,J=2.9 Hz, 1H), 6.79 (dd, J=9.7, 2.9 Hz, 2H), 5.38 (s, 1H), 5.34 (s, 1H),5.20 (quin, J=1.4 Hz, 1H), 5.14 (quin, J=1.4 Hz, 1H), 4.79 (s, 4H), 4.15(br. s., 2H), 3.89 (br. s., 2H), 3.33 (s, 12H), 2.65-2.75 (m, 2H), 2.58(m, J=7.6 Hz, 2H), 1.74-1.89 (m, 4H), 1.72 (s, 3H), 1.67 (s, 3H), 0.63(s, 6H).

Preparation of Compound 59

Compound 59 was synthesized from intermediates 42-2 and 51-2 followingthe general procedure V. HPLC-MS: m/z 1188.2 (calcd. 1187.6 for M⁺).UV/Vis: λ_(max)=650 nm.

Preparation of Compound 61

Compound 61 was synthesized form 1,3-diiodobenzene and intermediates49-1 and 35-7 following general procedures X, III, and XV, as outlinedin the scheme above. HPLC-MS: m/z 1162.2 (calcd. 1161.6 for M⁺). UV/Vis:λ_(max)=705 nm.

Preparation of Compound 62

Compound 62 was synthesized form 1,3-diiodobenzene and intermediates45-1 and 35-7 following general procedures X, III, and XV, as outlinedin the scheme above. HPLC-MS: m/z 1190.3 (calcd. 1189.6 for M⁺). UV/Vis:λ_(max)=680 nm.

Preparation of Compounds 54 and 71

Preparation of Compound 54-1

A solution of aryl bromide 19-5 (6.0 g, 11 mmol) and TMEDA (0.8 mL, 5.3mmol) in anhydrous THF (100 mL) was cooled to −78° C. under argon. Tothis solution tert-BuLi (c=1.52 M in pentane, 8 mL, 12 mmol) was addeddropwise over 5 min and the mixture was stirred at −78° C. for 5 min,followed by rapid addition of trimethylborate (1.6 mL, 14.4 mmol). Thereaction mixture was allowed to warm up to room temperature and thenquenched with MeOH (5 mL). The solvents were removed under reducedpressure and the residue was purified by flash chromatography (SiO₂,eluted with gradient from 5% to 20% EtOAc in hexanes). Desired boronicacid 54-1 was obtained (4.87 g, 87% yield) as a pale yellow solid.

General Procedure XXIII. Suzuki-Miyaura Coupling with Dihaloarenes.Preparation of Compound 54-2

Suspension of anthracene boronic acid 54-1 (1.0 g, 2.0 mmol) and2,4-dibromothiophene (0.17 mL, 1.5 mmol) in degassed EtOH (80 mL) wasrefluxed under argon until all solids were dissolved. Pd(PPh₃)₄ (50 mg,0.043 mmol) and 2 M aqueous Na₂CO₃ (2.1 mL, 4.2 mmol) were added andrefluxing was continued under argon for 4 h. Then the solvent wasremoved under reduced pressure, the residue was dissolved in DCM (50 mL)and filtered through Celite®. Filtrate was concentrated and the residuewas purified by flash chromatography (SiO₂, gradient elution from 10% to40% DCM in hexanes). Title compound 54-2 was obtained (565 mg, 60%yield) as a bright yellow solid.

Compound 54 was prepared from intermediate 54-2 and 11-3 followinggeneral procedures XVI, XVIIA, and XV, as outlined in the scheme above.HPLC-MS: m/z 1144.1 (calcd. 1143.6 for M⁺). UV/Vis: λ_(max)=660 nm. ¹HNMR (400 MHz, MeOH-d₄) δ ppm 8.34 (d, J=8.6 Hz, 1H), 8.27 (d, J=8.6 Hz,1H), 8.19 (d, J=8.2 Hz, 1H), 7.82 (d, J=9.0 Hz, 1H), 7.58-7.64 (m, 2H),7.53-7.58 (m, 4H), 7.46-7.53 (m, 1H), 7.41 (d, J=2.8 Hz, 2H), 7.38-7.44(m, 2H), 7.29-7.38 (m, 4H), 7.16-7.24 (m, 1H), 7.08 (t, J=7.2 Hz, 1H),6.86 (dd, J=9.8, 2.9 Hz, 2H), 5.35 (s, 1H), 5.36 (s, 1H), 5.17 (quin,J=1.3 Hz, 2H), 4.68 (br. s, 2H), 4.65 (br. s, 2H), 4.09 (br. s., 2H),3.91 (br. s., 2H), 3.36 (s, 12H), 3.02 (t, J=6.5 Hz, 2H), 2.92-2.99 (m,2H), 2.65-2.74 (m, 2H), 2.53-2.65 (m, 2H), 1.77-1.89 (m, 2H), 1.67-1.76(m, 2H), 1.70 (s, 6H), 0.65 (s, 6H).

Compound 71 was prepared from intermediate 54-1 and2,4-dibromo-5-methylthiophene, following the same sequence of reactionsas outlined for compound 54. HPLC-MS: m/z 1158.2 (calcd. 1157.6 for M⁺).UV/Vis: λ_(max)=660 nm. ¹H NMR (400 MHz, MeOH-d₄) δ ppm 8.35 (d, J=8.9Hz, 1H), 8.23 (d, J=8.8 Hz, 1H), 8.28 (d, J 9.1 Hz, 1H), 7.78 (d, J=9.4Hz, 1H), 7.49 (d, J=9.8 Hz, 2H), 7.47-7.60 (m, 4H), 7.41 (d, J=2.8 Hz,2H), 7.37-7.43 (m, 1H), 7.28-7.37 (m, 4H), 7.17-7.25 (m, 2H), 7.10 (td,J=7.5, 1.1 Hz, 1H), 6.89 (dd, J=9.6, 2.8 Hz, 2H), 5.36 (s, 2H), 5.17(quin, J=1.3 Hz, 2H), 4.70 (br. s., 4H), 4.09 (br. s., 2H), 3.92 (br. s,2H), 3.37 (s, 12H), 3.02 (t, J 6.6 Hz, 2H), 2.94-3.00 (m, 2H), 2.65-2.72(m, 2H), 2.62 (m, J=5.6 Hz, 2H), 2.28 (s, 3H), 1.81-1.89 (m, 2H), 1.70(s, 6H), 1.65-1.75 (m, 2H), 0.66 (s, 3H), 0.64 (s, 3H).

Preparation of Compound 63

Compound 63 was prepared from 2-bromo-4-iodotoluene and intermediates54-1, and 11-3 following general procedures XXIII, XVI, XVIIA, and XV,as outlined in the scheme above. HPLC-MS: m/z 1152.3 (calcd. 1151.6 forM⁺). UV/Vis: λ_(max)=650 nm. ¹H NMR (400 MHz, MeOH-d₄) d ppm 8.47 (br.s., 1H), 8.14-8.30 (m, 2H), 8.04 (d, J=7.9 Hz, 1H), 7.81 (d, J=7.7 Hz,1H), 7.71 (d, J=9.5 Hz, 1H), 7.58 (d, J=1.8 Hz, 1H), 7.51 (d, J=8.2 Hz,1H), 7.31-7.51 (m, 5H), 7.29 (d, J=2.8 Hz, 2H), 7.15-7.23 (m, 2H), 7.18(d, J=9.6 Hz, 2H), 7.03-7.15 (m, 3H), 6.70 (dd, J=9.7, 2.9 Hz, 2H), 5.29(quin, J 0.8 Hz, 1H), 5.22 (quin, J=0.8 Hz, 1H), 5.10 (quin, J=1.3 Hz,1H), 5.02 (quin, J=1.3 Hz, 1H), 4.58 (br. s, 2H), 4.54 (br. s, 2H), 3.98(br. s., 2H), 3.74 (s, 2H), 3.23 (s, 12H), 2.89 (t, J=6.6 Hz, 2H), 2.74(t, J=6.9 Hz, 2H), 2.51-2.62 (m, 2H), 2.37-2.49 (m, 2H), 2.05 (s, 3H),1.65-1.76 (m, 4H), 1.63 (m, J=1.5, 0.7 Hz, 3H), 1.55 (dd, J=1.5, 1.0 Hz,3H), 0.54 (s, 3H), 0.53 (s, 3H).

Preparation of Compound 64

Compound 64 was prepared from intermediates 63-3 and 53-2 following thegeneral procedure V. HPLC-MS: m/z 1366.3 (calcd. 1365.6 for M⁺). UV/Vis:λ_(max)=650 nm. ¹H NMR (600 MHz, MeOH-d₄; mixture of two rotamers) δ ppm8.12-8.31 (m, 2H), 7.86-8.03 (m, 3H), 7.71-7.77 (m, 2H), 7.60-7.71 (m,6H), 7.53-7.60 (m, 3H), 7.47-7.53 (m, 1H), 7.36-7.44 (m, 2H), 7.30-7.36(m, 2H), 6.88 (d, J=8.3 Hz, 1H), 5.47 (s, 1H), 5.35 (s, 1H), 5.26 (s,1H), 5.14 (s, 1H), 4.70 (br. s, 4H), 3.36 (s, 12H), 3.08 (br. s., 2H),2.96 (br. s., 2H), 2.69-2.77 (m, 4H), 2.67-2.69 (m, 4H), 2.65 (br. s,6H), 2.48 (br. s, 6H), 1.87-1.98 (m, 2H), 1.79-1.85 (m, 2H), 1.78 (s,3H), 1.71 (s, 3H), 1.66 (s, 3H), 0.68 (s, 3H), 0.64 (s, 3H).

Preparation of Compound 65

Compound 65 was prepared from intermediates 63-2 and 43-1, following thegeneral procedures XVIIA and XV, as outlined in the scheme above.HPLC-MS: m/z 1476.3 (calcd. 1475.8 for M^(t)). UV/Vis: λ_(max)=650 nm.

Preparation of Compound 69

Compound 69 was prepared from intermediates 63-1 and 56-1, following thegeneral procedures XVI, XVIIA, and XV, as outlined in the scheme above.HPLC-MS: m/z 1204.3 (calcd. 1203.7 for M⁺). UV/Vis: λ_(max)=660 nm. ¹HNMR (400 MHz, MeOH-d₄) δ ppm 8.15-8.44 (m, 2H), 7.94-8.05 (m, 1H),7.85-7.94 (m, 2H), 7.78-7.85 (m, 1H), 7.69-7.78 (m, 3H), 7.54-7.69 (m,8H), 7.27-7.38 (m, 1H), 7.19 (d, J=10.3 Hz, 2H), 6.75 (d, J=9.7 Hz, 2H),5.28 (br. s, 1H), 5.29 (br. s, 1H), 5.14 (br. s, 1H), 5.10 (br. s., 1H),4.80 (br. s., 2H), 3.69 (t, J=6.1 Hz, 4H), 3.18-3.27 (m, 2H), 3.23 (s,6H), 3.00-3.16 (m, 8H), 2.94 (t, J=6.6 Hz, 2H), 2.18 (s, 3H), 2.06-2.15(m, 4H), 1.90-2.06 (m, 2H), 1.74-1.90 (m, 2H), 1.58 (s, 3H), 1.59 (s,3H), 0.80 (s, 3H), 0.80 (s, 3H).

Preparation of Compound 82

Silaxanthone 82-1 was prepared as described in the literature (Umezawa,K.; Yoshida, M.; Kamiya, M.; Yamasoba, T.; Urano, Y. Nat. Chem. 2016, 9(3), 279-286).

Intermediate 82-2 was prepared from intermediates 63-1 and 82-1following the general procedure XVI.

Preparation of Compound 82-3

General method of deallylation of silicon-substituted xanthene dyes wasdescribed in literature (Umezawa, K.; Yoshida, M.; Kamiya, M.; Yamasoba,T.; Urano, Y. Nat. Chem. 2016, 9 (3), 279-286). According to thismethod, bis-allyl intermediate 82-2 (158 mg, 0.166 mmol) was dissolvedin MeOH (5 mL) and treated with the excess of solid NaBH₄ until thecolor turned yellow-green (gas released upon addition of NaBH₄). Themixture was stirred for additional 10 min, and then the mixture wasquenched with water and the resulting slurry was partitioned with EtOAc.Aqueous layer was discarded, organic layer was washed with brine, driedover anhydrous Na₂SO₄, filtered, and concentrated under reducedpressure. The residue was dissolved in degassed DCM (10 mL).1,3-Dimethylbarbituric acid (DMBA; 245 mg, 1.57 mmol) and Pd(PPh₃)₄ (43mg, 0.037 mmol) were added, and the mixture was stirred at ambienttemperature for 16 h. Then chloranil (49 mg, 0.20 mmol) was added, andafter 20 min of stirring the reaction mixture was filtered throughCelite®. The filtrate was concentrated under reduced pressure, and theresidue was purified by flash chromatography (SiO₂, eluted with gradientfrom 2% to 30% MeOH in DCM). Desired intermediate 82-3 was obtained as adark-blue solid (150 mg, quant. yield).

Compound 82 was prepared from intermediate 82-3, following the generalprocedures XVIIA and XV, as outlined in the scheme above. HPLC-MS: m/z1124.1 (calcd. 1123.6 for M+H⁺). UV/Vis: λ_(max)=625 nm.

Preparation of Compound 83

Compound 83 was prepared from the intermediates 82-4 and 51-2, followingthe general procedure V. The neopentyl glycol protecting group wasspontaneously removed during reversed phase purification. HPLC-MS: m/z1174.1 (calcd. 1173.6 for M+H⁺). UV/Vis: λ_(max)=625 nm. ¹H NMR (400MHz, MeOH-d₄) δ ppm 8.66 (br. s., 1H), 8.41 (d, J=9.5 Hz, 1H), 8.45 (d,J=8.4 Hz, 1H), 8.30 (d, J=7.8 Hz, 1H), 8.06 (d, J=1.3 Hz, 1H), 8.01 (s,1H), 7.96 (m, J=8.7 Hz, 2H), 7.47-7.73 (m, 7H), 7.32-7.46 (m, 3H), 7.23(d, J=2.3 Hz, 2H), 6.66 (dd, J=9.4, 2.3 Hz, 2H), 5.48 (s, 1H), 5.41 (s,1H), 5.27 (quin, J=1.3 Hz, 1H), 5.20 (quin, J=1.3 Hz, 1H), 4.98 (br. s.,2H), 4.59 (br. s, 2H), 4.29 (br. s., 2H), 4.05 (br. s., 2H), 3.35 (s,6H), 3.04-3.12 (m, 2H), 2.99 (t, J=6.5 Hz, 2H), 2.83-2.92 (m, 2H),2.72-2.83 (m, 2H), 2.16 (s, 3H), 1.87-1.98 (m, 4H), 1.79 (s, 3H), 1.72(s, 3H), 0.60 (s, 3H), 0.58 (s, 3H).

Preparation of Compound 66

Compound 66 was prepared from 2-bromo-6-iodotoluene and intermediates54-1 and 11-3, following the general procedures XXIII, XVI, XVIIA, andXV, as outlined in the scheme above. HPLC-MS: m/z 1152.3 (calcd. 1151.6for M⁺). UV/Vis: λ_(max)=650 nm. ¹H NMR (400 MHz, MeOH-d₄) δ ppm 8.51(s, 1H), 8.40-8.47 (m, 1H), 8.38 (d, J 10.0 Hz, 1H), 7.50-7.65 (m, 6H),7.36-7.45 (m, 2H), 7.40 (d, J=3.2 Hz, 2H), 7.21-7.36 (m, 5H), 7.31 (d,J=9.5 Hz, 2H), 7.17 (m, J=6.7 Hz, 2H), 6.87 (dd, J=9.8, 2.7 Hz, 2H),5.37 (s, 1H), 5.34 (s, 1H), 5.18 (m, J=1.7, 1.7, 1.7, 1.7 Hz, 2H), 4.94(br. s, 2H), 4.82 (br. s., 2H), 4.17 (br. s, 2H), 3.95 (br. s, 2H), 3.37(s, 12H), 3.04 (t, J=6.9 Hz, 2H), 3.00 (t, J=6.4 Hz, 2H), 2.73-2.82 (m,2H), 2.57-2.71 (m, 2H), 2.04 (s, 3H), 1.88-1.97 (m, 2H), 1.79-1.88 (m,2H), 1.70 (s, 6H), 0.65 (s, 3H), 0.61 (s, 3H).

Preparation of Compound 67

Compound 67 was prepared from intermediates 66-3 and 53-2 following thegeneral procedure V. HPLC-MS: m/z 1366.4 (calcd. 1365.6 for M⁺). UV/Vis:λ_(max)=650 nm.

Preparation of Compound 73

Compound 73 was prepared from 3-bromo-5-iodotoluene and intermediates54-1 and 11-3, following the general procedures XXIII, XVI, XVIIA, andXV, as outlined in the scheme above. HPLC-MS: m/z 1152.3 (calcd. 1151.6for M⁺). UV/Vis: λ_(max)=650 nm. ¹H NMR (400 MHz, MeOH-d₄; mixture oftwo rotamers) δ ppm 8.25-8.39 (m, 2H), 8.07-8.20 (m, 2H), 7.75-7.84 (m,2H), 7.61 (m, J=5.0 Hz, 2H), 7.47-7.54 (m, 1H), 7.39-7.46 (m, 3H), 7.37(m, J=3.2 Hz, 3H), 7.26-7.34 (m, 3H), 7.18-7.25 (m, 3H), 7.15 (d, J=5.6Hz, 1H), 6.78 (dd, J=9.7, 2.9 Hz, 2H), 5.36 (s, 1H), 5.34 (s, 1H),5.17-5.21 (m, 1H), 5.11-5.16 (m, 1H), 4.61 (br. s., 4H), 4.06 (br. s,2H), 3.83 (br. s, 2H), 2.97-3.03 (m, 2H), 2.90-2.95 (m, 12H), 2.85 (t,J=6.3 Hz, 2H), 2.63-2.70 (m, 2H), 2.61 (s, 3H), 2.49-2.59 (m, 2H),1.78-1.85 (m, 2H), 1.73-1.78 (m, 2H), 1.65-1.69 (m, 6H), 0.63 (s, 6H).

Preparation of Compound 74

Compound 74 was prepared from intermediates 73-3 and 53-2 following thegeneral procedure V. HPLC-MS: m/z 1366.6 (calcd. 1365.6 for M⁺). UV/Vis:λ_(max)=650 nm. ¹H NMR (400 MHz, MeOH-d₄) δ ppm 8.23 (s, 1H), 8.16-8.26(m, 1H), 8.06-8.15 (m, 1H), 7.96-8.06 (m, 1H), 7.52-7.79 (m, 11H), 7.41(d, J=3.0 Hz, 2H), 7.45 (d, J=9.9 Hz, 2H), 7.25 (s, 1H), 6.89 (d, J=9.3Hz, 2H), 5.45 (s, 1H), 5.34 (br. s., 1H), 5.24 (s, 1H), 5.13 (br. s.,1H), 4.48-4.70 (m, 4H), 4.38 (br. s, 2H), 3.91 (br. s., 2H), 3.36 (s,12H), 3.00 (s, 3H), 2.95-3.05 (m, 2H), 2.85-2.95 (m, 2H), 2.65-2.74 (m,4H), 2.63 (br. s., 6H), 2.47 (br. s, 6H), 1.84-1.94 (m, 2H), 1.77 (s,3H), 1.72-1.84 (m, 2H), 1.66 (s, 3H), 0.68 (s, 3H), 0.65 (s, 3H).

Preparation of Compound 75

Compound 75 was prepared from 1,5-dibromo-2,4-dimethylbenzene andintermediates 54-1 and 11-3, following the general procedures XXIII,XVI, XVIIA, and XV, as outlined in the scheme above. HPLC-MS: m/z 1166.4(calcd. 1165.6 for M⁺). UV/Vis: λ_(max)=650 nm. ¹H NMR (400 MHz,MeOH-d₄; mixture of two rotamers) δ ppm 8.45-8.53 (m, 2H), 8.25-8.44 (m,2H), 7.63 (d, J=9.3 Hz, 1H), 7.52-7.60 (m, 2H), 7.49 (d, J=6.8 Hz, 1H),7.44 (s, 1H), 7.40 (dd, J=6.8, 2.0 Hz, 1H), 7.37 (d, J=2.9 Hz, 2H), 7.33(d, J=9.7 Hz, 2H), 7.17-7.31 (m, 4H), 7.06-7.17 (m, 3H), 6.84 (dd, J9.7, 2.9 Hz, 2H), 5.36 (br. s., 1H), 5.35 (s, 1H), 5.19 (quin, J=1.3 Hz,1H), 5.15 (quin, J=1.3 Hz, 1H), 4.91 (br. s., 2H), 4.75 (br. s., 2H),4.18 (br. s., 2H), 3.83 (br. s, 2H), 3.34 (s, 12H), 3.03 (t, J=6.5 Hz,2H), 2.91 (t, J=6.4 Hz, 2H), 2.76 (dd, J=9.0, 6.7 Hz, 2H), 2.58 (dd,J=8.5, 6.7 Hz, 2H), 2.49 (s, 3H), 2.11 (s, 3H), 1.84-1.96 (m, 2H),1.75-1.84 (m, 2H), 1.72 (s, 3H), 1.68 (s, 3H), 0.61 (s, 3H), 0.58 (s,3H).

Preparation of Compound 76

Compound 76 was prepared from intermediates 75-3 and 53-2 following thegeneral procedure V. HPLC-MS: m/z 1380.4 (calcd. 1379.6 for M⁺). UV/Vis:λ_(max)=650 nm. ¹H NMR (400 MHz, MeOH-d₄) δ ppm 8.46 (br. s., 1H),8.34-8.41 (m, 1H), 8.22-8.30 (m, 1H), 7.74-7.78 (m, 1H), 7.63-7.72 (m,3H), 7.47-7.62 (m, 6H), 7.44 (s, 1H), 7.35-7.38 (m, 2H), 7.30-7.35 (m,1H), 7.34 (s, 1H), 7.28 (br. s, 1H), 6.88 (dd, J 9.6, 2.7 Hz, 2H), 5.40(s, 1H), 5.40 (s, 1H), 5.22 (quin, J=1.3 Hz, 1H), 5.18 (quin, J 1.3 Hz,1H), 4.91 (br. s., 2H), 4.27 (br. s., 2H), 4.08 (br. s., 2H), 3.36 (s,12H), 3.05 (t, J=6.6 Hz, 2H), 2.94 (t, J=6.7 Hz, 2H), 2.77-2.86 (m, 2H),2.68-2.73 (m, 2H), 2.55 (s, 6H), 2.52 (s, 3H), 2.47 (s, 6H), 2.12 (s,3H), 1.80-1.95 (m, 4H), 1.73 (s, 3H), 1.71 (s, 3H), 0.61 (s, 6H).

Preparation of Compound 77

Compound 77 was prepared from 2-bromo-4-iodoanisole and intermediates54-1 and 11-3, following the general procedures XXIII, XVI, XVIIA, andXV, as outlined in the scheme above. HPLC-MS: m/z 1168.4 (calcd. 1167.6for M⁺). UV/Vis: λ_(max)=650 nm. ¹H NMR (400 MHz, MeOH-d₄) δ ppm 8.77(d, J=2.4 Hz, 1H), 8.38-8.49 (m, 2H), 8.26 (m, J=8.0 Hz, 1H), 8.05 (d,J=9.5 Hz, 1H), 7.62-7.69 (m, 1H), 7.49-7.62 (m, 3H), 7.47 (d, J=8.0 Hz,1H), 7.42 (m, J=8.7 Hz, 1H), 7.26-7.39 (m, 4H), 7.17-7.24 (m, 2H), 7.14(d, J=8.7 Hz, 2H), 6.93 (d, J=2.9 Hz, 2H), 6.85 (d, J=8.6 Hz, 1H), 6.71(dd, J=8.6, 2.9 Hz, 2H), 5.38 (s, 2H), 5.18 (s, 2H), 4.94 (br. s., 4H),4.29 (br. s., 2H), 4.02 (s, 2H), 3.20 (s, 3H), 3.02-3.10 (m, 4H), 2.93(s, 12H), 2.79-2.86 (m, 2H), 2.70-2.78 (m, 2H), 1.98-2.08 (m, 2H),1.90-1.96 (m, 2H), 1.71 (s, 3H), 1.70 (s, 3H), 0.57 (s, 3H), 0.45 (s,3H).

Preparation of Compound 86

Preparation of Compound 86-1

To a suspension of 3-bromo-5-iodobenzoic acid (6.0 g, 18.4 mmol) inanhydrous DCM (20 mL) oxalyl chloride (6.5 mL, 75.8 mmol) was addeddropwise, followed by catalytic amount of DMF (5 drops; gas release wasobserved shortly after addition of DMF). The reaction mixture wasstirred at ambient temperature for 30 min, after which the suspensionbecame clear orange solution. The solvent was removed under reducedpressure. The residue was extensively dried under high vacuum, and thenredissolved in anhydrous DCM (30 mL) and added dropwise to a mixture of2-amino-2-methylpropan-1-ol (5.05 g, 56.7 mmol) and anhydrous DCM (20mL), while cooling the reaction mixture with ice/water bath (0° C.). Thereaction mixture was allowed to reach ambient temperature and stirredfor 3 h. The resulting suspension was filtered and the white precipitatewas additionally washed with DCM (30 mL). Combined filtrate and washingwere concentrated under reduced pressure to afford crude amideintermediate as a red oil. This was dissolved in neat thionyl chloride(13 mL) and the mixture was stirred at ambient temperature for 2 h. Thenexcess of thionyl chloride was removed in vacuo and resulting residuewas purified by flash chromatography (SiO₂, eluted with gradient from 5%to 10% of EtOAc in hexanes). The product (6.16 g, 89% yield) wasobtained as a white crystalline solid.

Compound 86-3 was obtained from oxazoline 86-1, anthracene boronic acid54-1, and silaxanthone 11-3, following the general procedures XXIII, andXVI (no TMEDA added for the latter), as outlined in the scheme above.

General Procedure XVIIB. Double Amination of TBDMS Diether. Preparationof Compound 86-4

A solution of bis-TBDMS ether 86-3 (40 mg, 0.041 mmol) in anhydrous DCM(2 mL) was treated with 1 M SOCl₂ in DCM (0.25 mL, 0.25 mmol) at ambienttemperature for 16 h. The solvent was then removed under reducedpressure, and the residue was extensively dried under high vacuum. Thecrude residue was dissolved in anhydrous DCM (2 mL) and added dropwiseto a mixture of 2-(methylaminomethyl)-phenylboronic acid (110 mg, 0.67mmol), K₂CO₃ (100 g, 0.72 mmol), and NaI (6 mg, 0.04 mmol) in anhydrousDMF (3 mL). The mixture was stirred at ambient temperature for 16 h.Then the mixture was filtered, the filtrate was concentrated underreduced pressure, and the residue was purified by reversed-phase flashchromatography (C18 SiO₂, eluted with gradient from 5% to 75% MeOH inwater+0.05% TFA). The title compound (24 mg, 52% yield) was obtained asa dark-blue oil.

Preparation of Compound 86-5

Oxazoline 86-4 (24 mg, 0.021 mmol) was dissolved in 6 N HCl (5 mL), andthe mixture was heated at 80° C. for 16 h. Then the reaction mixture wasdiluted with saturated NH₄Cl and neutralized with 25% NH₃ (aq) to pH˜3-4. Aqueous mixture was extracted with DCM, combined extracts weredried over anhydrous Na₂SO₄, filtered and concentrated under reducedpressure. The residue was additionally purified by reversed phase flashchromatography (C18 SiO₂, eluted with gradient from 5% to 75% MeOH inwater+0.05% TFA) yielding the title compound (11.7 mg, 52% yield) as adark-blue solid.

Preparation of Compound 86

A mixture of carboxylic acid 86-5 (11.7 mg, 0.011 mmol), EDC.HCl (7.5mg, 0.04 mmol), HOBt hydrate (2.15 mg, 0.014 mmol), APMA.HCl (6.5 mg,0.036 mmol), and DIPEA (0.02 mL, 0.11 mmol) in anhydrous DMF (1 mL) wasstirred at ambient temperature for 16 h. Then the reaction mixture wasdiluted with water, acidified with TFA and directly loaded onto C18 SiO₂column for flash chromatography purification (eluted with gradient from5% to 100% MeOH in water+0.05% TFA). The title compound (8.2 mg, 62%yield) was obtained as a dark-blue amorphous solid. HPLC-MS: m/z 1084.1(calcd. 1083.6 for M⁺). UV/Vis: λ_(max)=650 nm. ¹H NMR (400 MHz,MeOH-d₄) δ ppm 8.35 (br. s., 2H), 8.02-8.15 (m, 2H), 7.97 (br. s., 1H),7.84-7.93 (m, 2H), 7.72-7.82 (m, 2H), 7.67 (m, J=6.1 Hz, 3H), 7.56-7.63(m, 3H), 7.46-7.56 (m, 2H), 7.43 (d, J 2.9 Hz, 2H), 7.30 (d, J=9.7 Hz,2H), 7.22-7.36 (m, 1H), 6.84 (dd, J=9.7, 2.8 Hz, 2H), 5.70 (s, 1H), 5.59(br. s, 2H), 5.55 (br. s, 2H), 5.35 (quin, J=1.3 Hz, 1H), 4.81 (br. s,2H), 4.84 (br. s, 2H), 3.56 (t, J=5.7 Hz, 2H), 3.39 (t, J=6.5 Hz, 2H),3.36 (s, 12H), 2.83 (s, 3H), 2.78 (s, 3H), 1.91-1.95 (m, 2H), 1.92 (s,3H), 0.66 (s, 3H), 0.65 (s, 3H).

Preparation of Compound 25

Intermediate 25-1 was prepared from,1-bromo-4-[2-(trimethylsilyl)-ethynyl]benzene and intermediate 11-3 perthe general procedure X followed by a basic workup.

General Procedure XXIV. Sonogashira Coupling. Preparation of Compound25-2

A mixture of aryl alkyne 25-1 (250 mg, 0.61 mmol), aryl bromide 35-6(374 mg, 0.73 mmol), Pd(PPh₃)₂C₁₂ (43 mg, 0.06 mmol), copper(I) iodide(12 mg, 0.06 mmol), and triethylamine (2 mL) in degassed THF (15 mL) wasrefluxed under argon for 16 h. Then the reaction mixture wasconcentrated under reduced pressure, the residue was dissolved in MeOH,and filtered through Celite®. Filtrate was concentrated again and theresidue was purified by reversed phase flash chromatography (C18 SiO₂,eluted with gradient of MeOH in water+0.25% HCl) affording the titlecompound 25-2 (78 mg, 15%) as a brown oil.

Compound 25 was prepared from the intermediate 25-2 following thegeneral procedure V, as outlined in the scheme above. HPLC-MS: m/z1162.4 (calcd. 1161.6 for M⁺). UV/Vis: λ_(max)=650 nm.

Preparation of Compound 81

Intermediate 81-1 was prepared from intermediate 54-1 and ethyl5-bromo-2-thiophenecarboxylate following the general procedure XXIII.Intermediate 81-3 was prepared following the published procedure (Grimm,J. B.; Brown, T. A.; Tkachuk, A. N.; Lavis, L. D. ACS Cent. Sci. 2017, 3(9), 975-985).

Preparation of Compound 81-4

According to general method described in literature (Grimm, J. B.;Brown, T. A.; Tkachuk, A. N.; Lavis, L. D. ACS Cent. Sci. 2017, 3 (9),975-985), solution of intermediate 81-3 (46.7 mg, 0.10 mmol) inanhydrous THF (3 mL) was cooled to −78° C. under argon atmosphere. Tothe solution, tert-BuLi (1.52 M in pentane, 0.29 mL, 0.44 mmol) wasadded dropwise. The bright-yellow reaction mixture was stirred at −78°C. for 30 min and then warmed up to −20 OC. Solution of ethyl ester 81-1(140 mg, 0.225 mmol) in anhydrous THF (3 mL) was added slowly and thereaction mixture was allowed to warm up to ambient temperature andstirred for 16 h. The reaction was quenched with half-saturated NH₄Cl,acidified with 1 M HCl until dark-green color, and extracted with DCM(3×). Combined organic extracts were dried over anhydrous Na₂SO₄,filtered, and concentrated under reduced pressure. The residue waspurified by flash chromatography (SiO₂, eluted with gradient from 0 to25% MeOH in DCM) yielding the desired product (28 mg, 32%) as adark-green solid.

Compound 81 was prepared form intermediate 81-4, following generalprocedures XVIIA and XV. HPLC-MS: m/z 1144.1 (calcd. 1143.6 for M⁺).UV/Vis: λ_(max)=670 nm.

Preparation of Compound 68

Preparation of Compound 68-1.

Solution of aryl bromide 19-6 (555 mg, 1.02 mmol) and TMEDA (0.17 mL,1.14 mmol) in anhydrous THF (4 mL) was cooled to −78° C. under argon. Tothis solution t-BuLi (c=1.52 M in cyclohexane, 0.74 mL, 1.12 mmol) wasadded dropwise. After 5 min, tosyl azide (13.6% w/w in toluene, 1.6 mL,0.99 mmol) was added dropwise over 2 min. The reaction mixture wasstirred at −78° C. for 30 min and then was quenched by water (10 mL) andwas allowed to warm up to room temperature. Saturated NH₄Cl (10 mL) andDCM (15 mL) were added under vigorous stirring and then the layers wereseparated. Aqueous layer was discarded and organic layer wasadditionally washed with saturated NaHCO₃ and brine. Then the solutionwas dried over anhydrous Na₂SO₄, filtered, and concentrated underreduced pressure. The residue was purified by flash chromatography(SiO₂, eluted with gradient from 2% to 30% DCM in hexanes) affording2-azidoanthracene 68-1 (442 mg, 85% yield) as a yellow solid. Theproduct was stored under argon at −20° C. in the dark.

General Procedure XXV. Copper-Catalyzed Alkyne-Azide Cycloaddition.Preparation of Compound 68-2

A mixture of aryl alkyne 25-1 (86 mg, 0.19 mmol), aryl azide 68-1 (97mg, 0.19 mmol), copper(II) sulfate pentahydrate (9.5 mg, 0.038 mmol),TBTA (20 mg, 0.038 mmol), and sodium (L)-ascorbate (15 mg, 0.075 mmol)in anhydrous DMF (10 mL) was stirred at room temperature for 16 h. Thenthe reaction mixture was diluted with ethyl acetate (75 mL) and washedwith aqueous NH₄Cl (saturated solution diluted 1:10 with water, 100 mL),5% w/w aqueous LiCl (100 mL) and brine (50 mL). Organic layer was driedover anhydrous Na₂SO₄, filtered, and concentrated under reducedpressure. The residue was purified by flash chromatography (SiO₂, elutedwith gradient from 2% to 10% MeOH in DCM). This afforded titleintermediate 68-2 (78 mg, 43% yield) as dark blue solid.

Compound 68 was prepared from intermediate 68-2 following generalprocedures XVIIA and XV, as outlined in the scheme above. HPLC-MS: m/z1205.3 (calcd. 1204.6 for M⁺). UV/Vis: λ_(max)=650 nm.

Preparation of Compound 29

Intermediate 29-1 was prepared from intermediate 35-6 andethynyltrimethylsilane following the general procedure XXIV followed bybasic workup. Compound 29 was prepared from intermediates 29-1 and 2-2following the general procedures XXIV and V, as outlined in the schemeabove. HPLC-MS: m/z 1376.6 (calcd. 1375.6 for M+H⁺). UV/Vis: λ_(max)=650nm.

Preparation of Compound 70

The preparation of intermediate 70-1 was accomplished based on theprocedures reported for analogous compounds (Bertozzi, C. R.; Shieh, P.U.S. Pat. No. 9,410,958).

Preparation of Compound 70-1

Solution of 3-bromo-4-methylaniline (1.10 g, 5.9 mmol) in anhydrous THF(30 mL) was cooled to −78° C. under argon atmosphere. LiHMDS (1.05 M inTHF, 11.8 mL, 12.4 mmol) was added dropwise over 10 min. The reactionmixture was allowed to warm up to ambient temperature, stirred for 15min, and then was cooled back to −78° C. under argon atmosphere.Chlorotrimethylsilane (1.6 mL, 12.6 mmol) was added dropwise over 10min, and the reaction mixture was allowed to warm up to ambienttemperature and stirred for 1 h. Then the solvent was removed underreduced pressure. The resulting residue was suspended in hexanes,filtered, and the filtrate was concentrated under reduced pressure. Thecrude product 70-1 (1.85 g, 95% yield) was obtained as a brown-orangeliquid after thorough drying under high vacuum. The product was used inthe next step without further purification.

Preparation of Compound 70-2

Crude TMS-protected aniline 70-1 (1.85 g, 5.6 mmol) was dissolved inanhydrous THF (15 mL), and the solution was cooled to −78° C. underargon atmosphere. tert-BuLi (1.52 M in pentane, 4.5 mL, 6.84 mmol) wasadded dropwise and the solution was stirred at −78° C. for 30 min. Thensolution of silaxanthone 11-3 (0.075 M in THF, 55 mL, 4.13 mmol) wasquickly added, and the reaction mixture was allowed to warm up toambient temperature. After 1 h of stirring, the reaction was quenchedwith 1 M HCl (16 mL) and the mixture was concentrated under reducedpressure. The residue was neutralized with saturated NaHCO₃ (100 mL) andthen aqueous slurry was extracted with DCM (5×25 mL). Combined organicextracts were dried over anhydrous Na₂SO₄, filtered, and concentratedunder reduced pressure. The residue was purified by flash chromatography(SiO₂, eluted with gradient from 2 to 20% of MeOH in DCM), affording thedesired Si-rhodamine 70-2 (0.75 g, 40% yield) as a blue solid.

Preparation of Compound 70-3

A solution of aniline 70-2 (0.20 g, 0.44 mmol) in a mixture of glasialacetic acid and water 2:1 (v/v) was cooled to 0° C. To this mixtureNaNO₂ (46 mg, 0.67 mmol) was added as solid, and the mixture was stirredat 0° C. for 5 min, followed by addition of NaN₃ (60 mg, 0.92 mmol). Thereaction mixture was allowed to warm up to ambient temperature over 1.5h, at which point the reaction was complete. The reaction mixture wasslowly poured into 20% (w/v) aqueous Na₂CO₃ (100 mL) and the resultingslurry was extracted with DCM (3×). Combined organic extracts were driedover anhydrous Na₂SO₄, filtered, and concentrated under reducedpressure. Desired product 70-3 was obtained as a dark-blue solid withoutpurification (190 mg, 86%).

Compound 70 was prepared from intermediates 70-3 and 29-1 in accordancewith general procedures XXV and XV as outlined in the scheme above.HPLC-MS: 1219.3 (calcd. 1218.6 for M⁺). UV/Vis: λ_(max)=650 nm. ¹H NMR(400 MHz, MeOH-d₄) δ ppm 9.05 (br. s., 1H), 8.62 (br. s., 1H), 8.04-8.32(m, 4H), 7.85-8.02 (m, 2H), 7.71 (d, J=8.8 Hz, 1H), 7.42-7.50 (m, 3H),7.37-7.42 (m, 3H), 7.26-7.37 (m, 5H), 7.24 (d, J=9.6 Hz, 2H), 7.14 (t,J=6.6 Hz, 1H), 6.82 (d, J=9.1 Hz, 2H), 5.36 (s, 1H), 5.30 (s, 1H), 5.15(quin, J=1.3 Hz, 1H), 5.10 (quin, J=1.2 Hz, 1H), 4.42-4.71 (m, 4H), 4.00(br. s., 4H), 3.33 (s, 12H), 2.92-3.03 (m, 2H), 2.84-2.92 (m, 2H),2.60-2.68 (m, 2H), 2.54-2.60 (m, 2H), 2.18 (s, 3H), 1.77-1.84 (m, 2H),1.75 (s, 2H), 1.69 (s, 3H), 1.64 (s, 3H), 0.63 (s, 3H), 0.65 (s, 3H).

Preparation of Compound 72

The compound 72 was synthesized via the same steps described forcompound 70, starting from 4-bromoaniline and intermediates 11-3 and29-1 (see the scheme above). HPLC-MS: 1205.5 (calcd. 1204.6 for M⁺).UV/Vis: λ_(max)=650 nm.

Preparation of Compound 32

Compound 32 was prepared from 4-iodobenzaldehyde, 2,4-dimethylpyrrole,and intermediate 29-1 following the general procedures VII, XXIV, and V,as outlined in the scheme above. HPLC-MS: m/z 1102.0 (calcd. 1101.6 forM+H⁺). UV/Vis: λ_(max)=500 nm. ¹H NMR (400 MHz, MeOH-d₄) δ ppm 8.42 (d,J=8.5 Hz, 2H), 8.28 (d, J=8.8 Hz, 2H), 7.85 (d, J=8.0 Hz, 2H), 7.48-7.63(m, 4H), 7.44 (d, J=8.0 Hz, 2H), 7.36-7.48 (m, 3H), 7.20-7.36 (m, 4H),6.09 (s, 2H), 5.37 (s, 1H), 5.35 (s, 1H), 5.20 (quin, J=1.5 Hz, 1H),5.16 (quin, J=1.5 Hz, 1H), 4.51-4.76 (m, 4H), 4.04 (br. s., 2H), 3.97(s, 2H), 3.02 (t, J=7.0 Hz, 4H), 2.67 (t, J=7.4 Hz, 2H), 2.56-2.63 (m,2H), 2.51 (s, 6H), 1.74-1.90 (m, 4H), 1.72 (s, 3H), 1.70 (s, 3H), 1.52(s, 6H).

Preparation of Compound 34

Compound 34 was prepared from benzene-1,4-diboronic acid andintermediates 1-2 and 35-6, following the general procedures III (twice)and V, as outlined in the scheme above. HPLC-MS: m/z 1212.6 (calcd.1211.7 for M⁺). UV/Vis: λ_(max)=635 nm. ¹H NMR (400 MHz, CDCl₃) δ ppm8.14-8.44 (m, 5H), 8.08 (br. s., 1H), 7.95 (br. s., 1H), 7.83 (t, J=8.3Hz, 3H), 7.68 (d, J=7.9 Hz, 1H), 7.30-7.51 (m, 15H), 7.07-7.15 (m, 3H),5.86 (d, J=14.0 Hz, 2H), 5.37 (s, 2H), 5.34 (s, 1H), 5.32 (s, 1H), 5.11(br. s, 2H), 5.09 (br. s, 2H), 4.54 (s, 2H), 4.51 (s, 2H), 3.94 (br. s,3H), 3.92 (br. s, 3H), 3.39-3.43 (m, 2H), 2.88-2.93 (m, 2H), 2.46-2.62(m, 4H), 1.82 (s, 12H), 1.69 (s, 3H), 1.67 (s, 3H), 1.52-1.63 (m, 4H).

Preparation of Compound 30

Compound 30 was prepared from 4-ethynylphenylboronic acid andintermediates 2-2 and 35-6 following the general procedures XXIV, III,and V, as outlined in the scheme above. HPLC-MS: m/z 1452.0 (calcd.1451.7 for M+H⁺). UV/Vis: λ_(max)=650 nm. ¹H NMR (400 MHz, MeOH-d₄) δppm 8.45 (d, J=14.0 Hz, 2H), 7.90-8.04 (m, 3H), 7.72-7.75 (m, 1H),7.60-7.70 (m, 3H), 7.37-7.59 (m, 13H), 7.16-7.37 (m, 7H), 6.78 (d,J=14.0 Hz, 2H), 5.38 (s, 1H), 5.37 (s, 1H), 5.17 (br. s, 1H), 5.15 (s,1H), 4.40-4.53 (m, 4H), 3.09 (t, J=7.2 Hz, 4H), 3.03 (t, J=6.6 Hz, 4H),2.41 (quin, J=7.7 Hz, 4H), 1.68-1.72 (m, 3H), 1.67 (s, 3H), 1.26-1.33(m, 16H).

Preparation of Compound 31

Intermediate 31-1 was prepared from intermediate 14-4 following thegeneral procedure XIX.

Preparation of Compound 31-2

A mixture of bis-bromomethyl anthracene 31-1 (520 mg, 1.33 mmol),APMA.HCl (711 mg, 4.0 mmol), and potassium carbonate (1.57 g, 8.0 mmol)in anhydrous DMF (40 mL) was stirred at room temperature for 5 h. Thesolvent was then removed under reduced pressure. The residue wasresuspended in minimal amount of MeOH and filtered. Filtrate was dilutedwith 0.1 M HCl and purified by reversed phase flash chromatography (C18SiO₂, gradient of MeOH in water+0.25% HCl). This afforded intermediate31-2 (118 mg, 17%) as a yellow oil.

Intermediate 31-3 was prepared from 31-2 following the general procedureV.

Preparation of Compound 31

A mixture of carboxylic acid 31-3 (11 mg, 0.014 mmol), Cy5 amine 2-3 (11mg, 0.015 mmol), HOBt (2 mg, 0.015 mmol), EDC (3 mg, 0.016 mmol), andtriethylamine (3 mg, 0.03 mmol) in anhydrous DCM (4 mL) was stirred atroom temperature for 24 h. Then the reaction mixture was concentratedand the residue was purified by reversed phase flash chromatography (C18SiO₂, eluted with gradient from 10% to 100% MeOH in water). Thisafforded compound 31 (15 mg, 70% yield) as dark blue solid. HPLC-MS: m/z1487.9 (calcd. 1484.7 for M+H⁺). UV/Vis: λ_(max)=650 nm.

Preparation of Compound 38

Preparation of Compound 38-1

The mixture of 2-bromo-9,10-dimethylanthracene 35-2 (2.5 g, 8.8 mmol),acetyl chloride (0.89 mL, 13.7 mmol), and anhydrous aluminum chloride(1.68 g, 12.6 mmol) in anhydrous DCM (200 mL) was stirred at ambienttemperature for 24 h. Then water (200 mL) was added and layers wereseparated. Aqueous layer was additionally extracted with DCM (4×100 mL).The combined extracts were dried over anhydrous MgSO₄, filtered, andconcentrated under reduced pressure. The residue was purified by flashchromatography (SiO₂, eluted with gradient from 0 to 100% of DCM inhexanes). The product was obtained as a bright-yellow solid; ˜1:5mixture of 6-acetyl and 7-acetyl regioisomers (2.74 g, 95%).

Preparation of Compound 38-2

The mixture of intermediate 38-1 (2.74 g, 9.6 mmol), N-bromosuccinimide(3.76 g, 21 mmol), and AIBN (5 mg, 0.03 mmol) was refluxed in anhydrousCCl₄ (120 mL) for 3 h. Then the reaction mixture was concentrated underreduced pressure. The residue was triturated with MeOH (200 mL).Collected solid was dried under high vacuum to yield the desired product38-2 (3.27 g, 70%) as a yellow-orange powder.

Preparation of Compound 38-3

To the suspension of APMA.HCl (9.9 g, 56 mmol) and K₂CO₃ (21 g, 155mmol) in a mixture of anhydrous DCM and MeCN (1:1 v/v, 200 mL) that waspre-stirred at ambient temperature for 3 h, solid intermediate 38-2 (3.0g, 6.2 mmol) was added. The reaction mixture was vigorously stirred atambient temperature for 18 h. Then the reaction mixture was filtered andthe filtrate was concentrated under reduced pressure. The residue waspurified by reversed-phase flash chromatography (C18 SiO₂, eluted withgradient from 0 to 25% of MeOH in 0.1% HCl). Yield: 2.2 g (59%) of freebase as a yellow solid; ca. 8:3 mixture of regioisomers.

Compound 38 was prepared from 38-3 and 26-1 according to the generalprocedures XII, III, and V, as outlined in the scheme above. HPLC-MS:m/z 1180.2 (calcd. 1179.6 for M⁺). UV/Vis: λ_(max)=650 nm.

Preparation of Compound 41

Preparation of Compound 41-1

A mixture of 2,6-dibromoanthraquinone (5.24 g, 14.4 mmol) and CsF (2.40g, 15.8 mmol) in anhydrous DMSO (300 mL) was heated at 140° C. in aclosed vessel under argon atmosphere for 6 h and then the mixture wascooled to ambient temperature. Diethylamine (3.0 mL, 2.1 mmol) and K₂CO₃(3.98 g, 28.8 mmol) were added, and the reaction was continued at 50° C.for 48 h. Then the reaction mixture was diluted with water (1.5 L) andextracted with DCM (5×200 mL). Combined extracts were washed with brineand concentrated under reduced pressure. The residue was purified byflash chromatography (SiO₂, eluted with gradient from 0 to 100% of EtOAcin hexanes). The product 41-1 was obtained as a red solid (1.63 g, 32%).

Preparation of Compound 41-2

The solution of anthraquinone 41-1 (1.63 g, 5.68 mmol) in anhydrous THF(100 mL) was cooled to −78° C. under argon atmosphere. MeLi (1.6 M, 7.8mL, 12.5 mmol) was added dropwise over 10 min, and the reaction wascontinued for 1 h at −78° C. Then the reaction mixture was allowed towarm up to room temperature, and was quenched with saturated NH₄Cl. Theslurry was diluted with water and extracted with diethyl ether. Theextract was concentrated under reduced pressure and the residue waspurified by flash chromatography (SiO₂, eluted with gradient from 0 to25% EtOAc in DCM). The purified intermediate diol was dissolved in THF(30 mL) and added dropwise to the mixture of SnCl₂ (9.48 g, 42 mmol) in1 M HCl (20 mL) and diethyl ether (100 mL) at ambient temperature. Thereaction mixture was stirred for 1.5 h and then diluted with water (100mL), basified with 1 M NaOH to pH ˜4. Layers were separated and theaqueous layer was additionally extracted with DCM. Combined ether layerand DCM extracts were concentrated under reduced pressure, and theresidue was purified by flash chromatography (SiO₂, eluted with gradientfrom 0% to 20% of MeOH in DCM). Yield: 118 mg (6%) as an orange solid.

Compound 41 was synthesized from intermediate 41-2, following thesequence of general procedures XIX, XI, XIII, X, XIV, and XV, asoutlined in the scheme above. HPLC-MS: m/z 1133.4 (calcd. 1132.6 forM⁺). UV/Vis: λ_(max)=660 nm.

Preparation of Compounds 87 and 88

Silaxanthone 87-2 was synthesized from diiodosilaxanthone 87-1 and1-Boc-piperazine according to the method described in literature(Myochin, T.; Hanaoka, K.; Iwaki, S.; Ueno, T.; Komatsu, T.; Terai, T.;Nagano, T.; Urano, Y. J. Am. Chem. Soc. 2015, 137 (14), 4759-4765).

Intermediate 87-3 was synthesized from bromoanthracene 19-5,silaxanthone 87-2, and 2-(aminomethylamino)phenylboronic acid, followingthe general procedures XVI and XVIIB, as outlined in the scheme above.

Preparation of Compound 87-4

Solution of bis-Boc-protected intermediate 87-3 (66.4 mg, 0.054 mmol) inDCM (2 mL) was treated with TFA (0.5 mL) at ambient temperature for 1 h.The solvent was then removed under argon stream and the residue wasextensively dried under high vacuum. The crude product was used in thenext step without further purification.

Preparation of Compound 87

A solution of crude intermediate 87-4 (0.025 mmol) and triethylamine(0.03 mL, 0.22 mmol) in anhydrous DMF (3 mL) was treated with acryloylchloride (0.01 mL, 0.12 mmol) at ambient temperature under argonatmosphere. After 2 h, the reaction mixture was poured intohalf-saturated aqueous NaHCO₃ and the mixture was extracted with DCM.Combined extracts were dried over anhydrous Na₂SO₄, filtered, andconcentrated under reduced pressure. The residue was purified byreversed-phase chromatography (C18 SiO₂, eluted with gradient from 5% to100% MeOH in water+0.05% TFA). The title product was obtained (12 mg,42% yield) as a dark-blue solid. HPLC-MS: m/z 1030.1 (calcd. 1029.5 forM⁺). UV/Vis: λ_(max)=660 nm.

Preparation of Compound 88

A solution of crude intermediate 87-4 (0.025 mmol) and triethylamine(0.03 mL, 0.22 mmol) in anhydrous DMF (3 mL) was treated withmethacrylic anhydride (0.02 mL, 0.13 mmol) at ambient temperature underargon atmosphere. After 2 h, the reaction mixture was poured intohalf-saturated aqueous NaHCO₃ and the mixture was extracted with DCM.Combined extracts were dried over anhydrous Na₂SO₄, filtered, andconcentrated under reduced pressure. The residue was purified byreversed-phase chromatography (C18 SiO₂, eluted with gradient from 5% to100% MeOH in water+0.05% TFA). The title product was obtained (8.5 mg,29% yield) as a dark-blue solid. HPLC-MS: m/z 1058.1 (calcd. 1057.5 forM⁺). UV/Vis: λ_(max)=660 nm.

Synthesis of Hydrogel H (DMA/PEGDAAm/AAm)

DMA (N,N-Dimethylacrylamide) (23.6 uL), AAm (acrylamide) (23.6 mg),PEGDAAm (Poly-ethylene glycol diacrylamide) (20.3 mg),2,2′-Azobis[2-(2-imidazolin-2-yl)propane]dihydrochloride (0.75 mg), Dye(16.7 uL of 90 mM stock solution in DMSO), and water (65.1 uL) weremixed together until a homogenous solution was obtained. In some cases,some water was substituted for DMSO to increase solubility. The monomermix was purged with argon for 1 minute to remove oxygen. The solutionwas then injected in between two glass plates separated by a 0.01″-0.02″thick Teflon spacer, and held together with binder clips. The filledplates (hydrogel mold) were then placed in a desiccator and vacuumpurged with argon twice (vacuum was purged for 1 min for each cycle).The hydrogel mold was then heated in an argon purged oven at 45° C. for4 hours. The resulting hydrogel was removed from the mold and washedwith pH 7.4 PBS. The wash step consisted of shaking the gel (on anorbital shaker) in ˜50 mL of PBS for 2 hours during which the PBS wasexchanged 3×. A 5 mm-diameter disc was cut out of the gel slab using abiopsy punch and placed into a 96-well plate containing 150 uL of PBS.Absorbance and emission scans were taken of gel disc using aspectrofluorimeter.

Synthesis of Hydrogel A (AETACI/CEA/PEGDAAm)

AETACI ([2-(Acryloyloxy)ethyl]trimethylammonium chloride) (28.5 uL of an80 wt. % solution in H2O), CEA (2-carboxyethyl acrylate) (39 uL),PEGDAAm (Poly-ethylene glycol diacrylamide) (7.5 mg),2,2′-Azobis[2-(2-imidazolin-2-yl)propane]dihydrochloride (0.75 mg), Dye(16.7 uL of 90 mM stock solution in DMSO), DMSO (15 uL) and water (42.6uL) were mixed together until a homogenous solution was obtained. Themonomer mix was purged with argon for 1 minute to remove oxygen. Thesolution was then injected in between two glass plates separated by a0.01″-0.02″ thick Teflon spacer, and held together with binder clips.The filled plates (hydrogel mold) were then placed in a desiccator andvacuum purged with argon twice (vacuum was purged for 1 min for eachcycle). The hydrogel mold was then heated in an argon purged oven at 45°C. for 4 hours. The resulting hydrogel was removed from the mold andwashed with pH 7.4 PBS. The wash step consisted of shaking the gel (onan orbital shaker) in ˜50 mL of PBS for 2 hours during which the PBS wasexchanged 3×. A 5 mm-diameter disc was cut out of the gel slab using abiopsy punch and placed into a 96-well plate containing 150 uL of PBS.Absorbance and emission scans were taken of gel disc using aspectrofluorimeter.

Synthesis of Hydrogel B (HEMA/DMA/PEGDAAm)

HEMA (2-Hydroxyethyl methacrylate) (44.1 uL), DMA(N,N-Dimethylacrylamide) (29.4 uL), PEGDAAm (Poly-ethylene glycoldiacrylamide) (1.5 mg),2,2′-Azobis[2-(2-imidazolin-2-yl)propane]dihydrochloride (0.75 mg), Dye(16.7 uL of 90 mM stock solution in DMSO), DMSO (15 uL) and water (42.6uL) were mixed together until a homogenous solution was obtained. Themonomer mix was purged with argon for 1 minute to remove oxygen. Thesolution was then injected in between two glass plates separated by a0.01″-0.02″ thick Teflon spacer, and held together with binder clips.The filled plates (hydrogel mold) were then placed in a desiccator andvacuum purged with argon twice (vacuum was purged for 1 min for eachcycle). The hydrogel mold was then heated in an argon purged oven at 45°C. for 4 hours. The resulting hydrogel was removed from the mold andwashed with pH 7.4 PBS. The wash step consisted of shaking the gel (onan orbital shaker) in ˜50 mL of PBS for 2 hours during which the PBS wasexchanged 3×. A 5 mm-diameter disc was cut out of the gel slab using abiopsy punch and placed into a 96-well plate containing 150 uL of PBS.Absorbance and emission scans were taken of gel disc using aspectrofluorimeter.

Synthesis of Hydrogel C (DMA/PEGDAAm/AAm/Catalase/Reference Dye)

DMA (N,N-Dimethylacrylamide) (31.5 uL), AAm (acrylamide) (31.5 mg),PEGDAAm (Poly-ethylene glycol diacrylamide) (27 mg),2,2′-Azobis[2-(2-imidazolin-2-yl)propane]dihydrochloride (1 mg), Dye #21(16 uL of 50 mM stock solution in DMSO), CF₇₅₀-SE (14.6 uL of a 13.73 mMsolution in DMSO, with 15 mM triethylamine, and 20 mMaminopropylmethacrylamide), catalase (7 mg), and water (70 uL) weremixed together until a homogenous solution was obtained. The monomer mixwas purged with argon for 1 minute to remove oxygen. The solution wasthen injected in between two glass plates separated by a 0.015″ thickTeflon spacer, and held together with binder clips. The filled plates(hydrogel mold) were then placed in a desiccator and vacuum purged withargon 5 times (vacuum was purged for 1 min for each cycle). The hydrogelmold was then heated in an argon purged oven at 45° C. for 4 hours. Theresulting hydrogel was removed from the mold and washed with pH 7.4 PBS.The wash step consisted of shaking the gel (on an orbital shaker) in ˜50mL of PBS for 2 hours during which the PBS was exchanged 3 times. 5 mmlong×0.75 mm wide strips were out of the gel slab using a razor blade.

Measurement of Glucose In Vitro

Glucose sensors were prepared as described above (Sensors, A, B, C, orH). A 5 mm-diameter disc of hydrogel was placed into a well of aclear-bottom 96-well plate. 150 uL of PBS was added to the well, and theplate was inserted into a spectrofluorimeter and warmed to 37° C. At 37C, the fluorescence emission of the gel was collected (bottom readkinetic mode) every minute. Glucose solution was dispensed into the wellvia an injector module every 30 minutes to achieve final concentrationsof 50, 100, 200, and 400 mg/dL glucose. The fluorescence intensity ofthe gel's emission in response to each glucose level was measured.

Measurement of Glucose in Tissue

A glucose sensor was prepared as described above (Sensor C) and cut intoa rod measuring approximately 5 mm×0.75 mm×0.65 mm. The sensor rod wasinserted with an 18G needle into the subcutaneous tissue of a pig underanesthesia. FIG. 1 shows continuous glucose-sensing performance of thesensor in a live pig 28 days after implantation in the tissue. Forcomparison, reference blood glucose measurements were taken with acommercial glucometer every 5 minutes. The sensor data shown wascollected transcutaneously with a custom optical reader containing anLED excitation source and a fluorescence photodetector. FIG. 2 shows theplots of fluorescence signals of two sensors, both containing compound#21, a representative compound, implanted in the subcutaneous tissue ofan anesthetized pig. The sensor signals were read through the pig skinafter 28, 50, 57, and 109 days of in vivo implantation time. The meanabsolute relative difference (MARD) of the glucose values reported bythe sensor compared to that of actual blood glucose reference values wascalculated. The data demonstrates that the sensors exhibit long-termstability when implanted into a mammalian subcutaneous tissue.

All patents, patent applications and publications mentioned herein arehereby incorporated by reference in their entirety.

Although disclosure has been provided in some detail by way ofillustration and example for the purposes of clarity of understanding,it will be apparent to those skilled in the art that various changes andmodifications can be practiced without departing from the spirit orscope of the disclosure. Accordingly, the foregoing descriptions andexamples should not be construed as limiting.

TABLE 1 Com- Glucose Response pound (50 to 200 mg/dL): No Structure(I200 − I50)/I50 = 1

 7% 2

 9% 3

 0% 4

10% 5

 5% 6

10% 7

 5% 8

30% 9

25% 10

35% 11

20% 12

15% 13

 8% 14

 0% 15

 1% 17

15% 18

19% 19

10% 20

55% 21

27% 22

30% 23

 0% 24

 0% 25

 6% 26

24% 27

15% 28

 0% 29

 7% 30

17% 31

 1% 32

 4% 33

11% 34

17% 35

 0% 36

15% 37

15% 38

 2% 39

25% 40

27% 41

 2% 42

36% 43

38% 44

31% 45

 9% 46

 8% 47

10% 48

27% 49

10% 50

 2% 51

25% 52

26% 53

27% 54

55% 55

25% 56

10% 57

23% 58

45% 59

40% 60

 3% 61

 8% 62

14% 63

57% 64

44% 65

56% 66

28% 67

37% 68

 6% 69

27% 70

 9% 71

64% 72

 5% 73

42% 74

33% 75

36% 76

35% 77

61% 78

 5% 79

16% 80

 4% 81

19% 82

80% 83

48% 84

 0% 85

 0% 86

28% 87

 0% 88

 0%

What is claimed is:
 1. A compound of Formula I:

or a tautomer or a salt thereof, wherein the dotted lines denote a bondor absence of a bond; when the dotted line connecting R¹ and O is abond, R¹ is CX¹X² and R¹⁵ is absent; and when the dotted line connectingR¹ and 0 is absence of a bond, R¹⁵, at each occurrence, is independentlyH or C₁-C₆ alkyl, and R¹, at each occurrence, is H, optionallysubstituted C₁-C₆ alkyl, optionally substituted C₂-C₆ alkenyl,optionally substituted C₂-C₆ alkynyl, optionally substituted C₂-C₁₀heteroalkyl, polymerizable moiety, an NIR dye moiety, anelectron-withdrawing group, or an electron-donating group; X¹ and X² areindependently H or C₁-C₆ alkyl; R² is H or C₁-C₆ alkyl; Z is a C₆-C₁₄arylene optionally substituted with R¹¹, R¹², R¹⁴, and L²R¹³; R³, R⁴,R⁵, R⁶, R⁷, R⁸, R¹¹, R¹², R¹³ and R¹⁴ are independently H, optionallysubstituted C₁-C₆ alkyl, optionally substituted C₂-C₆ alkenyl,optionally substituted C₂-C₆ alkynyl, optionally substituted C₂-C₁₀heteroalkyl, polymerizable moiety, NIR dye moiety, electron-withdrawinggroup, or electron-donating group; R⁹ and R¹⁰ are independently H, C₁-C₆alkyl, polymerizable moiety, or NIR dye moiety; L¹, L², and L³ areindependently a bond or a linker group; and wherein at least one R¹, R³,R⁴, R⁵, R⁶, R⁷, R⁸, R⁹, R¹⁰, R¹¹, R¹², R¹³, or R¹⁴ is an NIR dye moietyand at least one R¹, R³, R⁴, R⁵, R⁶, R⁷, R⁸, R⁹, R¹⁰, R¹¹, R¹², R¹³, orR¹⁴ is a polymerizable moiety.
 2. The compound of claim 1, wherein thecompound has a structure of Formula IA, IB, or IC:

(IA), (IB)(IC), or a tautomer or a salt thereof.
 3. The compound ofclaim 1, wherein the electron-withdrawing group is selected from thegroup consisting of halogen, C(O)R′, COOR′, C(O)NH₂, C(O)NR′R″, CF₃, CN,SO₃H, SO₂CF₃, SO₂R′, SO₂NR′R″, ammonium, alkyl ammonium, and NO₂,wherein R′ and R″ are independently H or C₁-C₆ alkyl.
 4. The compound ofclaim 1, wherein electron-donating group is selected from the groupconsisting of NR^(N1)R^(N2), OR′, NHC(O)R′, OC(O)R′, phenyl, and vinyl,wherein R^(N1), R^(N2), and R′ are independently H or C₁-C₆ alkyl. 5.The compound of claim 1, wherein L¹, L², or L³ are, independently, abond or a linker group selected from optionally substituted amino,optionally substituted amido, —O—, optionally substituted —CH₂C₆H₄O—,C₂-C₂₀ PEG linker, optionally substituted C₆-C₁₀ arylene, optionallysubstituted five to ten member heteroarylene, optionally substituted—C₁-C₆ alkylene-Ar—, optionally substituted —C₂-C₆ alkenylene-Ar—,optionally substituted —C₂-C₆ alkynylene-Ar—, optionally substituted—C(O)NH—C₁-C₆ alkylene-Ar—, optionally substituted C₁-C₆alkylene-C(O)NH—C₁-C₆ alkylene-Ar—, —(CH₂CH₂O)_(n)—, —(CH₂CH₂O)_(p)CH₂CH₂—, optionally substituted C₁-C₁₀ alkyl, optionally substitutedC₂-C₁₀ alkenyl, optionally substituted C₂-C₁₀ alkynyl, and optionallysubstituted C₂-C₂₀ heteroalkyl, wherein n is an integer from 1 to 10, pis 2, 3, 4, or 5, and Ar is C₆-C₁₀ arylene or five to ten memberheteroarylene.
 6. The compound of claim 1, wherein L¹, L², or L³,independently comprises one or more substituents selected from acarboxylic group, a sulfonic acid group, ammonium, and an amino group.7. The compound of claim 1, wherein polymerizable moiety is selectedfrom —NH(CO)C(R)CH₂, —O(CO)C(R)CH₂, and CHCH₂, wherein R is H or C₁-C₃alkyl.
 8. The compound of claim 1, wherein the NIR dye moiety iscyanine, hemicyanine, fluorone, oxazine, phenanthridine, rhodamine,rosamine, indolium, quinolinium, benzophenoxazine, benzopyrillium,bisindoylmaleimide, boron-dipyrromethene, boron-aza-dipyrromethene,carbopyronins, perylene, porphyrin, ruthenium complex, lanthanidecomplex, benzoxanthenium, xanthene, fluorescein, squaraine, coumarin,anthracene, tetracene, pentacene, or pyrene dye residue.
 9. The compoundof claim 1, wherein the NIR dye moiety has the structure selected from:

or a tautomer or a salt thereof, wherein R^(N1) and R^(N2) areindependently C₁-C₁₀ alkyl optionally substituted with one or moregroups selected from —SO₃H, —SO₃ ⁻, —CO₂H, or —CO₂ ⁻, and

denotes the point of attachment to L².
 10. The compound of claim 1,wherein the NIR dye moiety has the structure of:

wherein R′, at each occurrence, is independently H, optionallysubstituted C₁-C₁₀ alkyl, optionally substituted C₂-C₁₀ alkenyl,optionally substituted C₂-C₁₀ alkynyl, or optionally substituted C₂-C₂₀heteroalkyl.
 11. The compound of claim 1, wherein the NIR dye moiety hasthe structure of:

wherein Y¹ is selected from O, P(O)R′, SiR′R″, and NR′, wherein R′ andR″ are independently H or C₁-C₆ alkyl; R²⁰ and R²¹ are independently H,C₁-C₆ alkyl, or R²¹ and R²⁰, together with the nitrogen atom to whichthey are attached, form a form a 6- or 5-membered ring optionallysubstituted with a polymerizable moiety; R²³ and R²⁴ are independentlyH, C₁-C₆ alkyl, or R²³ and R²⁴, together with the nitrogen atom to whichthey are attached, form a form a 6- or 5-membered ring optionallysubstituted with a polymerizable moiety; R²² and R²⁵ are independentlyH, C₁-C₆ alkyl, or R²¹ and R²², together with the atoms to which theyare attached, form a 6- or 5-membered ring, or R²⁴ and R²⁵, togetherwith the atoms to which they are attached, form a 6- or 5-membered ring;and R²⁶ and R²⁷ are independently H, C₁-C₆ alkyl, or R²⁶ and R²⁰,together with the atoms to which they are attached, form a 6- or5-membered ring, or R²⁷ and R²³, together with the atoms to which theyare attached, form a 6- or 5-membered ring.
 12. The compound of claim11, wherein Y¹ is SiMe₂.
 13. The compound of claim 1, wherein thecompound has the structure of Formula II:

or a tautomer or a salt thereof, wherein R¹, R², R³, R⁴, R⁵, R⁶, R⁷, R⁸,R⁹, R¹⁰, R¹¹, R¹², R¹⁴, R¹⁵, L¹, L² and L³ are as defined for compoundof Formula I, and wherein at least one R¹, R³, R⁴, R⁵, R⁶, R⁷, R⁸, R⁹,R¹⁰, R¹¹, R¹², R¹³, or R¹⁴ is an NIR dye moiety and at least one R¹, R³,R⁴, R⁵, R⁶, R⁷, R⁸, R⁹, R¹⁰, R¹¹, R¹², R¹³, or R¹⁴ is a polymerizablemoiety.
 14. The compound of claim 1, wherein the compound has astructure of Formula III:

or a tautomer or a salt thereof, wherein the dotted lines denote a bondor absence of a bond; when the dotted line connecting R¹ and O is abond, R¹ is CX¹X² and R¹⁵ is absent; and when the dotted line connectingR¹ and O is absence of a bond, R¹⁵, at each occurrence, is independentlyH or C₁-C₆ alkyl, and R¹, at each occurrence, is H, optionallysubstituted C₁-C₆ alkyl, optionally substituted C₂-C₆ alkenyl,optionally substituted C₂-C₆ alkynyl, optionally substituted C₂-C₁₀heteroalkyl, polymerizable moiety, NIR dye moiety, electron-withdrawinggroup, or electron-donating group; X¹ and X² are independently H orC₁-C₆ alkyl; R² is H or C₁-C₆ alkyl; R³, R⁴, R⁵, R⁶, R⁷, R⁸, R¹¹, R¹²,and R¹⁴ are independently H, optionally substituted C₁-C₆ alkyl,optionally substituted C₂-C₆ alkenyl, optionally substituted C₂-C₆alkynyl, optionally substituted C₂-C₁₀ heteroalkyl, polymerizablemoiety, NIR dye moiety, electron withdrawing group, or electron donatinggroup; R⁹, R¹⁰, and R¹³ are independently H, optionally substitutedC₁-C₆ alkyl, optionally substituted C₂-C₆ alkenyl, optionallysubstituted C₂-C₆ alkynyl, optionally substituted C₂-C₁₀ heteroalkyl,polymerizable moiety, or NIR dye; L¹, L², and L³ are independentlylinker group or a bond; and wherein at least one R¹, R³, R⁴, R⁵, R⁶, R⁷,R⁸, R⁹, R¹⁰, R¹¹, R¹², R¹³ or R¹⁴ is a polymerizable moiety.
 15. Thecompound of claim 14, wherein the electron-withdrawing group is selectedfrom the group consisting of halogen, C(O)R′, COOR′, C(O)NH₂, C(O)NR′R″,CF₃, CN, SO₃H, SO₂CF₃, SO₂R′, SO₂NR′R″, ammonium, alkyl ammonium, andNO₂, wherein R′ and R″ are independently H or C₁-C₆ alkyl.
 16. Thecompound of claim 14, wherein the electron-donating group is selectedfrom the group consisting of NR^(N1)R^(N2), OR′, NHC(O)R′, OC(O)R′,phenyl, and vinyl, wherein R^(N1), R^(N2), and R′ are independently H orC₁-C₆ alkyl.
 17. The compound of claim 14, wherein L¹, L², and L³, are,independently, a bond or a linker group selected from optionallysubstituted amino, optionally substituted amido, —O—, optionallysubstituted —CH₂C₆H₄O—, C₂-C₂₀ PEG linker, optionally substituted C₆-C₁₀arylene, optionally substituted five to ten member heteroarylene,optionally substituted —C₁-C₆ alkylene-Ar—, optionally substituted C₂-C₆alkenylene-Ar—, optionally substituted C₂-C₆ alkynylene-Ar—, optionallysubstituted —C(O)NH—C₁-C₆ alkylene-Ar—, optionally substituted —C₁-C₆alkylene-C(O)NH—C₁-C₆ alkylene-Ar—, —(CH₂CH₂O)_(n)—,—(CH₂CH₂O)_(p)CH₂CH₂—, optionally substituted C₁-C₁₀ alkyl, optionallysubstituted C₂-C₁₀ alkenyl, optionally substituted C₂-C₁₀ alkynyl, andoptionally substituted C₂-C₂₀ heteroalkyl, wherein n is an integer from1 to 10, p is 2, 3, 4, or 5, and Ar is C₆-C₁₀ arylene or five to tenmember heteroarylene.
 18. A polymer comprising one or more residues of acompound of claim
 1. 19. A sensor for detecting an analyte comprising apolymer, wherein the polymer comprises one or more residues of acompound of claim
 1. 20. A method of measuring blood glucoseconcentration in a mammalian subject, comprising: a) implanting a sensorof claim 19 into subcutaneous tissue of a mammalian subject; b)measuring at least one wavelength of light in theglucose-concentration-dependent luminescent signal from the sensor witha detector to produce a detected luminescent signal; and c) processingthe detected luminescent signal to produce a glucose concentration. 21.The compound of claim 1, wherein L¹, L², or L³ are, independently, abond or a linker group selected from optionally substituted amino,optionally substituted amido, —O—, optionally substituted —CH₂C₆H₄O—,C₂-C₂₀ PEG linker, optionally substituted C₆-C₁₀ arylene, optionallysubstituted C₅-C₁₀ heteroarylene, optionally substituted —C₁-C₆alkylene-Ar—, optionally substituted —C₂-C₆ alkenylene-Ar—, optionallysubstituted —C₂-C₆ alkynylene-Ar—, optionally substituted —C(O)NH—C₁-C₆alkylene-Ar—, optionally substituted —C₁-C₆ alkylene-C(O)NH—C₁-C₆alkylene-Ar—, —(CH₂CH₂O)_(n)—, optionally substituted C₁-C₁₀ alkyl,optionally substituted C₂-C₁₀ alkenyl, optionally substituted C₂-C₁₀alkynyl, optionally substituted C₂-C₂₀ heteroalkyl, wherein n is aninteger between 1 and 10 and Ar is C₆-C₁₀ arylene or C₅-C₁₀heteroarylene.
 22. The compound of claim 14, wherein L¹, L², and L³,are, independently, a bond or a linker group selected from optionallysubstituted amino, optionally substituted amido, —O—, optionallysubstituted —CH₂C₆H₄O—, C₂-C₂₀ PEG linker, optionally substituted C₆-C₁₀arylene, optionally substituted C₅-C₁₀ heteroarylene, optionallysubstituted —C₁-C₆ alkylene-Ar—, optionally substituted C₂-C₆alkenylene-Ar—, optionally substituted C₂-C₆ alkynylene-Ar—, optionallysubstituted —C(O)NH—C₁-C₆ alkylene-Ar—, optionally substituted —C₁-C₆alkylene-C(O)NH—C₁-C₆ alkylene-Ar—, —(CH₂CH₂O)_(n)—, optionallysubstituted C₁-C₁₀ alkyl, optionally substituted C₂-C₁₀ alkenyl,optionally substituted C₂-C₁₀ alkynyl, optionally substituted C₂-C₂₀heteroalkyl, wherein n is an integer between 1 and 10 and Ar is C₆-C₁₀arylene or C₅-C₁₀ heteroarylene.